Yes, 1.3 will be standalone. You will not need BF2 anymore to install PR:BF2. You just grab prbf2_1.3.0.0_full.iso, install it, and you're good to go with nothing more to do.
Those on 1.2.1 should be able to patch to 1.3, in which case your BF2 files may be modified slightly, but it shouldn't cause any issues with other mods such as ReviveBF2 and FH2. That said though, if you do play other mods, you should probably grab the full install and install PR:BF2 to a separate directory to avoid any future possible conflict.
Those who just play PR:BF2 may as well grab the full installer as well, uninstall BF2 and PR:BF2 1.2, and start fresh with 1.3. Will save you a few GB's of hard drive space. But yeah, the patch should be there, providing it works (still gotta test it, there might not be one if it breaks things, we'll see)
Legalities aside, it's about the only thing we can do to keep PR:BF2 alive at this time. We're not as ready as EA/DICE were to let our game die and all our hard work go to waste. And like others have said in the thread, abandonware, etc, I don't think EA will care too much. Of course, if they actually do care, their legal team is more than welcome to send us a cease and desist order, and we'll simply revert back to the way things are at the moment. Naturally, that'd do wonders for their public image.
But anyway, it's not like we've ever followed the EULA. Ever since we included the BF2:SF content in PR (when was that, 0.6?), we've been breaking the EULA. Add to that the 100p servers, the new master server, things like PRMumble, BUIS, and a whole bunch of other stuff... The list of things we've "illegally" done is actually rather large. I'm still yet to ever receive a single message from EA or DICE, so, well, shrug...
So to those looking to buy BF2, and you can wait and don't want to play other mods, you should probably hold off until we release 1.3. To the inevitable question of when 1.3 will be released, when it's ready

.