As Jorgemg1984 said, "most jazz records are recorded with everyone playing at the same time". However, personally, I don't think it's wrong or "cheating" (as some might say) to overdub. I think in a live context a group is what it is at that day and time but when you are recording you want to make the best, most exciting recording you can make, something that will stand up to repeated listenings. I'm not advocating protools-ing the life out of a recording, I just think recording can afford the artist opportunities to do things that they might not be able to do in a straight ahead context. I guess it all depends on what sound/concept you are going for.
Two examples of some great jazz that has resulted from experimentation with technology and overdubbing:
Lennie Tristano - "Lineup" - `
Bill Evans - "Conversations with myself" `
I think both of these tracks show that the improvisor can still respond to what's happening in context but after the fact.
So in answer to your question "Din", one other option would be to completely isolate certain sound sources. For example, if you are using a "proper" studio that will have separate isolation booths you could record with everyone playing live using headphones with the guitar amp, bass amp (and drums) all in individual rooms/spaces . In this instance you could take the live recording as is, if you are happy with everyones playing. If you're not happy with everyones playing you have the option to re-record small (or large) sections. For example, this would provide you the opportunity to try more adventurous solos that you might not have been willing to try (for whatever reason) while everyone was playing live.
With regard to multi-tracking - as in using a guide track and a click, getting the drums done, then the bass, then the guitars etc... It may result in a really tight recording but may also be a little characterless.
Hope that helps in terms of putting another view forward. I'm curious to see what the general consensus on recording jazz is here. Hopefully more people respond.
Best of luck with the recording.