1) You can software disable any card in Device Manager, Windows XP is smart enough to use the other one as default display (it doesn't have to be the one used for POST, you simply have to wait for Windows to boot in that case).
2) If you REALLY want to cut power COMPLETELY for given GPU (ie. 0W power usage no leds/fans, etc.), the only way is to have a board with PCI-e on/off switches (like EVGA X58 Classified), and additional switch(es) on cables that connect PCI-e power plugs to PSU.
You have to do this for all GPUs you want to control this way (don't worry - you can have one for few cables)
3) Most popular boards with all three standards (PCI-e, AGP, and PCI), are called 4CoreDual series 775Dual series, ALiveDual-eSATA2 and 939Dual series.
PS. When trying to plug switches for 6/8-pin PCI-e connectors :
DO NOT connect +12V to ground because you didn't checked where they go.

1) It seems to work without disabling the second card, but I do get the prompt after booting into Windows about the second card so thats probably the main reason why I should disable the other one, right? I will still need to multiboot I think, because I will need different drivers for each card and switching drivers require safe mode reboot AFAIK anyway (I am using the DDU program).

2) Good idea, I could rig some old drive bay fan controller as a switcher for the power cables. Are the PCIe switches on those EVGA boards physical only or also available as software? If physical only, then its also a small issue to look into.

Well, you don't have to disable it if driver(s) "are OK" with both working at the same time.
If you have problems with the one you don't want to use - sure, disable it (or PCI-e bridge it uses).
Multiboot from restart = You will get seperate drivers for each Windows.
If you use one driver on one Windows, you can install something else on the other OS.

Those are physical, in case of X58 Classified they are implemented as bridges to be exact :

Thank you very much, this was super helpful and seems to solve the current issue for me on WinXP system. I am assuming I can leave the power cables plugged in when I use this "PCIe disable" feature as in the fans would remain turned OFF? And would they still suck the power from PSU or is there some mechanism that will prevent that when "PCIe disable" mode is turned ON?

Just by the way, would you happen to know of an older board with the PCIe disable feature that supports AGP (and Win98) just like the EVGA example?

I never used it myself.
How card will react : Connect 6/8-pins to card, do not put it in PCI-e slot, and turn on the power on PSU. Result should be the same.

Also, PCI-e disable works ONLY on PCI-e powered stuff.
So, for example, if fan controller on given card is powered via 12V power and that 12V comes from 6-pin, it can still work (regardless of PCI-e connection).

X58 boards can work with Win98.
Sadly, I do not know of any pre LGA 1366 boards that have PCI-e switches.
This feature is usually only present on highest end boards (since it was designed for watercooling users and extreme OC'ers).

I would think there could be some boards that can do the switching in bios, I have seen some mentions on the web but nothing concrete.

If the fan will still spin even after "pcie disable" and I wont manage to switch off the 6-pin power, the fan could probably be replaced with 3rd party fan with its own power connector. But then what would be the point of the "pcie disable" feature if its still sucking power from somewhere meaning there will be some (small?) heat coming off the card components. I originally thought of doing only this (shutting down 3rd party fan) but its probably not a good idea to have a fully functioning card sit idle without the fan spinning, even when idle. It depends on the card of course, but I would rather find a solution that works with majority of cards.