Paired crystals or lots of crashes
The situation you have described is:
- a technologically primitive setting - no autopilots, even if they could interact with the telepathic crystals and lots of trouble seeing directly beneath any given island; and
- a village consisting of many islands (dozens?) which presumably need to stay quite close to each other but not keep crashing into each other.
If each island in the village independently determines its vector then there are going to be crashes. A human standing in the middle of an island at least a hundred metres across will not be able to eyeball perfectly whether they are stationary with respect to another island 50 metres away or whether they are closing at 10-15 centimetres per minute, so every night the village must either spread itself out widely or accept that there will be a collision somewhere in the village.
The simplest alternative I can see is that each flying island (or craft - see later) has its "motive" rune-embedded crystal linked to a "reference" rune-embedded crystal and the position of the island is determined with respect to its reference point. So the village centre has its reference crystal mounted either on the ground or on some really big (city?) flying island and the village controller moves the village to where it needs to be with respect to that. Each of the subordinate islands in the village has their reference crystal embedded in the village centre island, so once they move into their position relative to the centre they will remain there and the village will move as a whole. If you want there to be levitating "air boats" then each will have its reference crystal on its home island and it will define its movements with respect to that location. (If you don't want air boats then the islands will need to get very close and stay very still with respect to each other during transfers in order for gangplanks to be used.)
Wait, I hear you asking "but I want to know what it looks like!" My suggestion is that a pilot approaches their motive crystal, but doesn't touch it until they have selected and picked up in one hand a "pointer" crystal, with various sizes available. Large pointers are for big movements - with "big" meaning whatever you want depending on the demands of world and story - small for fine movements etc. The pilot then:
- Places their non-master hand on the motive crystal for their island/craft.
- Moves their pointer crystal around until it "clicks" (vibrates/lights up/sends telepathic pulse) at the moment that the pointer is in the correct position to reflect the current position of the island with respect to its reference crystal.
- Drags the pointer crystal to the new position the island needs to be in. If the crystal is dragged faster than the island can fly to the new related position or if the pilot breaks the physical connection with either the pointer or the motive crystal then the island will stop moving and step 2 must be repeated. Steady hands will be needed for a successful journey, with considerable strength also if a sufficiently heavy pointer (required for long distance travel) is being used.
- Listen out for the lookouts telling you to stop because the island or village is about to run into something!
Example: Tanner A is on a subordinate island of the village that is currently positioned level with the village centre with its motive stone 90m north of its reference stone. All the other subordinate islands in the immediate vicinity are also maintaining the same level as the village centre. The wind shifts to a northerly, blowing the stench of the tannery across the village. Tanner A is politely requested to move some distance to the south until the wind changes again.
Tanner A sets the assistant tanners as lookouts and then takes up his smallest pointer crystal, which works at 1:100 scale, in his right hand. He places his left hand on the motive crystal and slowly moves the pointer until it is 90 cm north of the motive crystal, moving it around gently until it clicks/flashes/whatever. He then slowly moves his pointer up 50 cm, raising the tannery island 50 m with respect to the village centre island. Maintaining the same height, he then slowly moves the pointer over the motive crystal until he is at nearly full arms reach, with the pointer 50 cm above and 100 cm south of the motive crystal.
Unfortunately, this leaves him directly over another subordinate island, so he needs to move further for politeness and safety (as people do not like tannery waste products falling on their homes) but his arm length does not let him move further with the smallest pointer. Breaking contact with his left hand, the tannery island stops moving for the moment. The tanner puts down the smallest pointer crystal and takes up a larger one, that works with a scale of 1:500. He returns his left hand to the motive crystal and even more carefully moves the pointer until it is 10 cm above and 20 cm south of the motive crystal, gently moving it around until it engages. Perspiration beads on his forehead as he agonisingly slowly moves the pointer another 20 cm to the south (40 cm south in total), then lowers it 10 cm until the tannery is at rest again at the same level as the rest of the village but with its motive crystal now 200 m south of its reference crystal on the village centre. The tanner removes his left hand from the motive crystal and puts the pointers back into their storage bag until the next time the wind changes...
Edit: Based on comments from the OP re level of conflict in this world, it's worth noting that any mechanism that allows flying stone islands to be piloted effectively also allows those islands to be used as massive kinetic energy weapons. The advantage of the solution I have proposed is to reduce the amount of accidental carnage, but I cannot think of an option that will prevent deliberate attacks. As a villager in this situation I would really want my village to be able to relocate and move away from the fighting.
If fighters are desired then one option could be to employ a squadron leader craft that has its reference crystal back at base but its squadron of small fighters (with their reference crystals on the squadron leader) can zip around with a fair degree of freedom within a few hundred metres of the leader without having to swap pointer crystals all the time. If a fighter can kill an enemy squadron's base craft then that will eliminate the entire squadron, so it is critical to correctly balance offensive action against defending your own leader. Weapons on fighters are well outside the scope of this question though...
