Recently UDPSoft -- developers of a popular gaming server browser The All-Seeing Eye -- included a custom filter option which allows users to include their own command line, player name and config for filters.
The All-Seeying Eye is available for download at
http://www.udpsoft.com/eye/It has tons of features and supports plenty of games.
On with the show.. First create a normal filter. Filter->New..
You'll want to insert the following code into the filter window, and name the filter with something practical... like Paintball 2.0
1 if servertype != "Q2" remove
2 if game ~== "pball" keep
3 remove
You should now have a new filter under your My Filters branch on the game/filters viewer. Select the newly created filter and do Filter->Custom config...
Once there you can browse to the paintball2.exe from the alpha release and insert any name you use if it differs from those of other games.
Now these servers should launch the newer alpha standalone rather than Quake 2.
If there are any questions feel free to reply or ask me on IRC.