The upgrades to FCS are ridiculously cheap compared to past upgrades plus you get all the studio apps as a bonus if you didn't have them already.
If you have a good reason to not upgrade right now, like an older CPU that can't handle Tiger and FCS 5.1.1 then the question becomes more about what format are you shooting and digitising and are you planning an offline/online workflow or finishing in FCP?
If for example you are shooting DV NTSC, I could see how capturing and then upgrading would be the path of least hassle. I wouldn't do any other work than capturing before the upgrade though. The info that is stored in the QT files themselves is the most important stuff like Reel Name and TC. You can get that by dragging the files into a browser window of a brand new 5.1.1 project and avoid any 4.1 legacy problems.
More complicated formats and 24p or Cinema Tools issues would make me really reconsider doing any of it in 4.1.
I would in go about it in this order:
1) Ensure that I can't upgrade right now.(Why? Money, Time, other projects still in 4.1...)
2) If I can't and I have to get started now, what is in FCS 5.1.1 that I would really need that 4.1 doesn't have. Do I need to upgrade at all for this project?
3) If I had to start now,and I needed 5.1 to finish and couldn't upgrade right now, I would start logging in 4.1. Save all the logs as Batch lists.
4) If I haven't upgraded after logging I could begin capturing.
5) After capturing I would upgrade or decide to finish in 4.1.
Something like that..