Several years ago I allowed my players (of which there were 5) to have up to two alternate characters in the campaign I was running. They were fighting in a civil war to overthrow a corrupt regime. They were based in an old castle (ala Suikoden) and could choose whichever character selection they wished to handle the missions.
This was a mixed bag. While it let the players try out different character designs, it prevented them from ever having that attachment that comes with fleshing out a character and roleplaying it for 20+ levels.
My advice: don't do it. Of course, my caveat is that if you have a group that prefers to hack and slash it might work out. If you have in depth stories (which these side quests tend to foster) then it's probably not the strategy you should go with. After all, if all you wanted were hack and slash you would just be playing 4E. Am I right?
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If you decide to do it, maybe try to do it over e-mail.
But my advice is to, as DM, find ways to avoid these kinds of situations.
If a Paladin PC in my campaign does something needful of atonement, I design the "side quest" as part of what the other PCs are doing -- exactly the way Faction Mission in Pathfinder Society works.
Something like that -- that can be handled quickly, as part of the "mission" or as something easily done over e-mail.
A few years ago, I was running a 3.5 game with some friends. They were all reletively inexperienced, but had all come up with wonderful back stories that I fully implemented with all of them to create side quests for them. My side quests pretty much ran the gamut of different possible ways to handle the situation. For example, one of the characters had a sidequest that had rather cohesively flowed into the main story, so no deviation was required from the main questline for the characters.
Another one dealt with the elf in the party going back to her homeland, where the humans/gnomes/etc. would be forbidden to follow. For this particular sidequest, I had written up a few NPC characters for the others to play (since the character was of the royal bloodline, the other players played her royal guardsmen) and the whole scenario played out rather swimmingly. I even had the opportunity to kill off the expendable NPC/PC characters by refusing to pull punches on them (I had been going a little easy on the group since they were all new). In the end, all of the players loved it.
The third and last one didn't end up being so much a side quest per se, but I worked together with him between games to deal with the "voices in his head".
I'd say your best bet is to try different ideas to keep the game moving forward, and try to avoid sidelining a player, even if you do have to sideline their character. Also, all of the above ideas were situations that were able to be fleshed out within one to two sessions, so if you do end up splitting the party, you wouldn't want it to go on too much longer than that, since playing a throwaway character could get very tedious very fast.
I must strongly disagree with KnightOfStyx.
While I did not Gms such things myself I did took part in a few such games and the players that enjoyed it the most were those who immersed themselves the most in roleplaying. Some of them had multiple characters in the same campaign, and sometimes played one-time characters issued them by GM (half-NPC as we usually called it).
I have seen players enjoying occasional switch and trying to play something different without giving up their regular character.
It wasn't in anything based on d20, however.
I must strongly disagree with KnightOfStyx.
While I did not Gms such things myself I did took part in a few such games and the players that enjoyed it the most were those who immersed themselves the most in roleplaying. Some of them had multiple characters in the same campaign, and sometimes played one-time characters issued them by GM (half-NPC as we usually called it).
I have seen players enjoying occasional switch and trying to play something different without giving up their regular character.It wasn't in anything based on d20, however.
YMMV