Note that a 1 km rock slamming into the earth from space could be a very bad day for everyone within a few hundred kilometers of it, but the physics aren't the same as suddenly displacing that much sea water and solid helium. Large extinction events on Earth are strongly correlated with 10km+ objects. They are so deadly, because they are large enough to impact the surface in tact. Smaller objects tend to break up and vaporize before impacting the surface. In this scenario, we have a large object that bypassed the Earth's atmospheric shield, and it's not anything like a natural object.
Unless this imaginary tech can first remove an equal volume of the water, before beaming in the 1km diameter sphere, it would have to displace all of that water, instantaneously. This would indeed be a very effective bomb. It would literally vaporize nearly a cubic kilometer of water, causing sufficient heat to rapidly melt the helium, which would add to the explosive effect and increase heating and pressure. A shockwave would travel back to the center of the sphere, heating more helium as it travels, and then bounce back outwards. Depending on the depth of the water, this shock wave will probably have sufficient force to vaporize or at least liquify all the remaining helium. How much water that would displace is a mathematical exercise I'll leave for someone else.
The total volume of displaced water would increase substantially as all that superheated fluid/gas expands. The shockwave from such an explosion would cause a rather large tsunami that would radiate in all directions at something like 1200 km/hr. and the shock wave passing through the lower levels of the ocean would probably kill everything for a considerable distance. The deeper your hero is, the more likely it is that the shockwave will destroy whatever vessel they are hiding in, or kill them directly if they are some kind of aquatic.
A rather large mushroom shaped cloud would rise up to at least the stratosphere, and a shockwave would travel outwards through the atmosphere. There would be a bright flash of light as a large volume of the atmosphere is suddenly ionized from the heat. All of this is nearly equivalent to a 1 km body of ice slamming into the earth, minus the momentum, but rather than being slowed, heated and exploding in the relatively thin atmosphere, it would encounter high pressure water immediately.
If any of the sphere survives in a solid or liquid state after the initial explosion, the sea will slam back into it and the subsequent shock wave would cause another explosion. The process would repeat until you had a very warm volume of sea water and helium bubbles, slowly dissipating heat to the surrounding water.
It's just a guess, but I'd say you probably don't want to be within a few thousand kilometers of such an event. There would probably be a large magma filled crater at the bottom of the ocean, that would also contribute to heating the area for quite a long time, and might spew sufficient toxic gases to cause a localized extinction event.
Come to think of it, the displacement of that much water will dissociate the water into mostly hydrogen and oxygen ions. The hydrogen would certainly fuse and possibly the oxygen as well. A 1/3 km hydrogen bomb core would be devastating.
So let's assume that the plot limits the rate of appearance of the object. We're already using more energy than a large cluster of starts give off in a lifetime, just teleporting that much mass over any distance. But it's not much of a bomb if it appears too gently, so you get to decide just how devastating this bomb is. In fact, it's the perfect weapon in that regard. Not only can you vary the size, you could vary the rate from say small fractions of the speed of light, all the way up to 99.999..%.
A more reasonable limit would a few tenths of the speed of light. Lowers the peak power requirements for the teleporter. Might even vary depending on the size. A large mass would have to have a lower rate than a small one.
So now you can dial-in the attack to a level that almost, but not quite extinguishes your hero.
If the hydrogen fuses, that might cause a sufficiently forceful implosion to fuse the helium! Now we're talking shattered planet.