MarkB
Legend
If I wanted a reason, I'd probably look to the weapon itself. I'd say something like the ultimate radiation/energy emitting from the weapon would slag any droid and fry any being close to it. Maybe the warhead starts to disintegrate before it gets to its destination (though....you can spend some real time in hyperspace--weeks).
I dunno.
Got any guesses?
Though I read quite a few of the comics way back when, I have no recollection of this particular doomsday weapon (let's face it, the EU is so littered with them, it's hard to pick one out), so I'm not particularly invested in looking for an explanation.
However, if you're after a rationalisation, then to build on your suggestion, maybe there's something about the warheads that's incompatible with hyperdrive engines - one will overload the other if they're in close proximity.
Therefore, the Galaxy Gun is needed to accelerate the missile and 'punch' it into hyperspace, after which it cruises on momentum until it reaches its target.