Giant post incoming!
If a civilization finds their sun thrown out of the galaxy, then I think it's kind of a bittersweet outcome. Obviously on the one hand they're much more isolated from other star systems, so unless they have some really nice FTL or long-term bio-stasis technology then they're kind of stuck there... but on the other hand that means they don't have to worry about the chance of getting wiped out by a nearby supernova or something of that sort. I'd think it's a better fate than plunging through the dense galactic center, honestly.
I can't say much for the question of radiation, because IIRC there's much about the galactic magnetic field that we don't know about yet. I can say that it's pretty much inevitable that the merger would send material towards the supermassive black holes at the center of the galaxies, thus causing a lot of accretion and giving off a great deal of radiation. Most of that radiation ends up being spewed out in polar jets though, so it might not be too big of an issue as that'd be directed away from us. But if we were sent through the galactic center, ehhhh... that might not be so healthy, but I wouldn't know. At the very least it'd make the night sky a lot more full of stars.

The effects on planetary systems is minimal at best. The distance between objects is great enough such that the chances of there being collisions between stars or planets is virtually nonexistent (though not strictly impossible). It actually shouldn't happen much more frequently than it does at any other time, since stars are orbiting the center of the galaxy somewhat haphazardly to begin with. Stars belonging to the halo and bulge especially, as their orbits are highly inclined relative to the disk.
For a more convincing argument of this, just look at globular clusters. The stars have chaotic spherical orbits and the star density is much higher than you'd find in most areas of two merging galaxies. Since we don't see signs of stars smashing each other in globulars, it's pretty safe to say that collisions must be extremely rare.
So with all the stuff that doesn't happen during a merger, what
does happen?
Well, although stars don't really hit one another, molecular clouds most certainly do, and this should trigger a burst of star formation. We see this happening pretty often actually, where a galaxy interacting with another one undergoes a fit of star formation. We call these starburst galaxies, and the
Antennae Galaxies are a great example.
Also, with the Milky Way and M31 being both large and comparable in size, we also expect that they will eventually form a single large elliptical galaxy, though this is a slower process. Eventually the tidal streams are essentially "smoothed out", leaving a big (probably spherical) agglomeration of stars. The burst of star formation will also end once most of the available gas has been either consumed or dispersed, and as the elliptical ages it will become yellower in color as the bluer, more massive stars die out.
tl;dr, mergers don't do much on the local scale. Stars don't really hit each other and planetary orbits are mostly undisturbed. The significant effects are generally on the galactic scale.
