[sionnsar]

So, what do they do with the reverse acceleration given the beam GENERATOR?

My thought exactly.

[beezdotcom]

Now, if they based the generator on the moon, that would be feasible for the outbound trip (the effects shouldn't become pronounced for thousands of years, anyway). But on the Mars side, they'd have few choices. Even if the rotations of Deimos and Phobos weren't a problem, their masses are small enough that this sort of constant gentle force could begin to perturb their orbits.