Getting the at the oil while it's still in the ground is prohibitive. Granted, despite what you said, a bacteria could do it. There are bacteria that can survive at high pressures, there's already bacteria that eat oil, and bacteria can multiply quickly to where it wouldn't be an immediate result, but would be an eventual result given enough time.
The problem here is three-fold:
- These type of resistance movements are rare and usually very small in number. (Most pro-environment people also believe in either pacifism or minimal violence). So they would not have the resources to genetically engineer the bacterium needed.
- These types of activities that are active usually target immediate-result targets meant to cripple a war-supporting arms of an oil-based military-industrial complex supply lines, and avoid the negative PR that comes from hurting people and most oil wells comes with guards.
- These rare people are usually lone-wolves who have just been pushed too far by resistance to improving the world's environment for some reason, and as such, their resources are only able to go after small targets like gas stations.
Also, there's another problem. You're using the word "terrorist", but having them attack infrastructure - not people. Terrorist activities are activities that have the goal of human death; they're meant to strike fear in a population (hence terrorism) and not merely a side-effect or non-event.
Actual Eco-terrorism is ridiculously rare and would be more like hunting down an Oil Baron or setting off a bomb at some fossil fuel convention/expo (which, in all fairness, would likely be much more effective, as CEOs are notoriously afraid of taking responsibility for their actions).
Further, as they're actively defending something (the environment and humanity's health) that was there first, aggressive political terms are not applicable, and generally require a defensive one to be accurate. Eco-"terrorists" would not exist without polluting industries.
Words like rebels, resistance movement, etc. are as such more accurate than terrorist.
So, our eco-rebels, targeting an active oil well is extremely far-fetched unless this is taking place in some alternate world. However, if that's the case, and there's some organization that's well funded and well supported and protecting of the planet comes at a greater moral ranking in their belief system than human life (such as AVALANCHE from Final Fantasy 7),then you may have something to work with.
So, assuming a fantasy organization with resources to oppose a military-industrial complex, there is a reasonable solution to "poisoning" oil wells.
First would be to develop a robotic mole without the restriction of requiring a feeder pipe behind it, something capable of tunneling down to oil reserves, so it can move along, seeding them with something to disrupt them. As an ecological organization, release of CO2 is antithetical to its goals, so this eco-terrorist group would not use a genetically engineered bacteria (which would release massive amounts of CO2). Instead, it'd use a genetically engineered archaea adding some of the DNA from oil-devouring bacteria, something that could survive at pressure, would be single-celled so as to help it move through the oil field, and could feed on the CO2 it generated to genetically designed to produce heat, oxygen, a non-oil carbon form (sugar, coal, diamonds, graphite, carbon nanostrings, Red #40, buckyballs, carbon nano-foam, etc.) - eventually solidifying an oil field and rendering it un-harvestable (carbon nanofoam would probably be the most effective). The mole could be fueled by by the oil (mildly ironic, but a small price to pay from their perspective), letting it run indefinitely according to its programming (restocking as Archea multply and re-fueling from the oil), and continue to seed areas whenever oil rigs are installed, permanently clogging the area around them and rendering them useless.