Your thoughts are correct. You can only turn on FTP and TFTP with the bootflags, thus requiring a reboot. Let's hope they fix that in a future release.
I can think of two methods:
1. You telnet into the switch, presumably using some sort of terminal program? If not, you can probably find a program on the 'net that will suit your purposes. Log into the switch, display the file, can't remember if its a "type" or "more" command to show the config/boot file, then do the old fashioned copy and paste into a local text file. Just be sure you copied all the lines properly.
2. The PCMCIA card is a standard ATA flash card. Its readable in most laptops. Copy the configs to the flash, pop the card out and into a laptop, then copy it off of there. You won't get any logs for the time period the flash card is out of the management card though.