What is the most practical method of upgrading the beta version we have installed to the full version of the Standard edition of ISA Server without losing any configurations already in place?
There are no *official* recommendations on this published on the MS site, so we can't say what is the preferred method for making the upgrade.
We have upgraded the RC1 directly, and we have done the same with the trial version. Most things seem to be "OK", but you really never know what's left in the registry and the system32 folder after doing this sort of thing.
If you're talking about a production machine, you best bet is to wipe the entire machine, reinstall Win2k, and then install the final version of ISA on that machine. By doing this, no "sins of the past" are left on the machine, which might complicate support and troubleshooting issues.