I think it'll be difficult to do a "full" system encryption after the setup, because you'd probably need to wipe your existing partitions during the process. A home partition might well work, because you don't actually need it to run the system, but root parititon is then a whole other story..whatever way there is, I think it involves running the system a while from someplace else than the actual installation, which makes it more or less the same as if you'd just reinstall the system. Also, if you do reinstall, you don't have to think about gimmicks, just take backups, do the job and push the backups back in. Easier, safer and for all I know, faster too.
Remember that even if you do encrypt your "whole" system, you'll still have to leave a small portion unencrypted (so you can boot), and that's the weak point. At present, nothing you do will make the system inpenetrable, if you're even a little paranoid. Though if your biggest worries are younger-than-teen kids and their pranks, you're all right.