There are (or were) servers with only ComputerCraft, and turtles are balanced perfectly fine for that. I don't think turtles can ever be balanced for FTB, because they'll either be cheaper than every other autominer (and therefore OP) or very expensive (and therefore useless for small tasks like turning off Dire's animal farm)
Not saying this should be done, but it would be possible to have like two sets of turtles, standard and advanced. Standard would cost as they currently do, but touching lava would destroy it and touching any other liquid, or having sand/gravel fall on it, would shut it off. Advanced would be made of like steel plates and rubber sheets and be immune to water/lava like they currently are. That way to get an effective and reliable miner you need the advanced one, but for tasks in controlled environments you would make do with the standard one.
Another way to balance would be giving standard turtles very small hard drives, so advanced programming wouldn't work on them, and have a more expensive hard drive upgrade.
Again, not saying this should be done, just giving an example of how it _could_ be implemented to be more balanced with the rest of the pack.