Using physics is not breaking the rules. If I drop a hammer on someone's head from 200 feet up in the air, that is not breaking the rules, that is using physics. I get tired of having to handwave almost every rule in Traveller because the rules were handwavium when they were written instead of actually being thought through. Giving something an acceleration and then saying that it can't move is what I would expect from someone who never took a science class, not someone writing a science-fiction game. So, let's fix the problem instead of using even more handwavium to cover up the original handwavium.
Why not just add a limitation the same as if you built it as a prototype M-Drive? Allow it to be built a TL earlier and make it only work out to like 10D from a gravity well. Doesn't something like that already exist for other things? I could have sworn I read this rule somewhere.