I think we decided it was fine for you to login multiple times if necessary, but just post to the forums so we knew not to login before you'd finished.
Sometimes it would be beneficial for players effectively working on the same 'team' to login to each other to move units, (as long as the players agree of course!) since it can keep the game moving. The only time it becomes a problem is if one player gains an advantage he shouldn't have for some reason. I can't think of many likely scenarios, but here are a few which might mean we shouldn't do this kind of thing on a regular basis:
1) If A logs in as B and B can see units from peaceful civ C that A can't then if C was planning to attack A it might mean they have knowledge they shouldn't have (because B would never have thought it necessary to warn A about C's units)
I would hope that if A and B are working together, B would always think it is necessary to warn A about C's units ...

Now if B and C are together planning to backstab A, then that is a whole new level of deceit ...
2) If A asks B if he can login to move his units but B was secretly planning on backstabbing A it becomes a difficult position for B since he can't really decline the offer without alerting A.
Hmm ... if he is backstabbing in the current turn, that could be tricky, but if it is some future plan, A presumably already knows what units B has that A wants to move, and where they are, so maybe allowing the cross-login is not so revealing?
3) A logs in as B and does a lot more than move a few units (eg. changing build queues, drafting units etc) which is something that, from a RP perspective, player B would never have done.
Unless this was requested during B's absence, it would be cause for summary execution!

I don't think any of the scenarios are particularly likely to happen, but if we allow this kind of thing as a general rule we have the potential to end up with 2 warring parties playing several civs each and everyone else just sitting back and watching! As long as it's regulated in some way (even just the usual gentlemanly conduct) we'll probably be fine though. We seem to have a good bunch of players happy enough to sort things out OOC if something has gone wrong.
As long as the minimum units needed for effective coordination are moved in a cross-login, we should be able to avoid the two player game scenario you describe. Alternatively, units can always be gifted as a means of improving coordination. Ideally the cross-logins would be minimal.
dV