It seems to be legal in the rules, but seems a bit odd thematically.

Situation:

Horton in Y-Wing with Ion Cannon vs Turr Phenirr

Horton uses his Ion cannon on Turr Phenirr. Turr Phenirr then attacks, which allows him to make a free boost action. Still, though, he is under the influence of the ION cannon.

As I said, technically the ION cannon only restricts the next chosen maneuver in the next maneuver phase. However, it just seems like the Ion effect really should also restrict other 'action' maneuvers while it is in effect.

Yeah, looking at the Ion Token card, I would say that Turr is able to perform his free Boost or Barrel Roll action in this situation. Having the Ion token doesn't restrict him from taking either of these two actions either after attacking, or even after maneuvering for that matter.

Maybe you can think of it this way:

The combat phase may be split into rounds but in real time the two fighters firing on each other take just a few seconds… so maybe Horton fires first and while the ion cannon shots (which we know will hit) are travelling towards Turr, Turr fires while doing a boost action! And in the middle of the boost action it the ion cannon shots hit and shorts out Turr for a couple of minutes!

How's that sound?

Well, excepting that unless the pilots have the same skill value, the shots are not simultaneous. Turr has already been hit with the ION cannon, has taken the point of damage, and gained the ION marker.

I suppose the explanation might be that the disabling effect of the ION cannon takes a little bit of time to 'disable' the ship's engines after it has hit a ship.

A bit of a stretch, but eh.

It is interesting as a side note, that this makes BOOST (and engine upgrades) even better (not just for Turr). The fact that an ION'd ship can still boost to move a bit farther than the ION move, or even start a turn in order to, say, avoid an obstacle or going off a table edge, is pretty huge.