Can I free Jaheira and Minsc from their cages, then tell them to meet up with me later? I dislike controlling so many characters at once, but I'd like to do their missions later. Is this possible?

I'm not sure if that's possible but you could just save the game before you try it. It should be obvious through their dialog whether they will hate you for abandoning them and leave forever, or say sth like "fine, I'll find my own way out and meet you at the nearest inn".

That said, the Baldur's Gate games are balanced around having a group of six adventurers working together, so you're probably better off getting used to controlling multiple characters.

IIRC, if you leave Minsc and Jaheira down there, they're lost forever.

You should get used to controlling 4 characters, since you're supposed to have a group of 6.

If you're good at the game and make a min-maxed PC, you can finish the game with less, you can even solo it, but it's not recommended for a first playthrough.

Actually, I am pretty sure that if you free them, but don't accept them into your party they will both be at the Copper Coronet later.

All of them can be safely dismissed, and will show up in Athkatla later. In general, in BG2, there's only a couple of rare cases where a character will leave your group permanently. If you kick them out of the party while they're dead, they're gone for good, but other than that you're unlikely to lose someone forever.

Each character has a specific location that they'll go to once you kick them out, unless you specifically tell them to "wait right here" when you kick em out.
Minsc and Yoshimo go to the Copper Coronet.
Jaheira goes to the big house in the southwest part of the Docks.
Imoen goes to Waukeen's Promenade, and later to the Copper Coronet.
Other characters have similar locations, and they'll generally tell you exactly where they're going when you boot them.