A lot of players weren't around during the rebel take over. Now it's so that the Spellguard invited people into their tower for safety, as the closest sanctuary to most around Upper. For those who weren't around during the event and entirely unwilling to fall to rebel hands, can it be assumed that those have taken up residence in the Tower during the assault? (Or elsewhere out of the city for that matter.)

Yes.

If a character was not present for something plot-significant, he just happened to be "away." When a character returns, he/she can decide what they want to do next. You wouldn't assume that they did anything at all in particular, just not present.