Nirth: Hehe, I doubt they went to the trouble to take it out just to appease Valve. I checked the wiki and you need to destroy an end game
boss so it will likely take a while before someone with a GOG version finds it.
Gengar78: well, for super time force ultra there are valve characters exclusive to the steam version (I heard there will be different characters for the playstation version) so I hope this wasn't a similar situation.
Re-logic isn't much for taking stuff out save for developer items(well they are still in the code but you will die if you equip them) like Red's Armor and Wings, Cenix's armor and Wings, ect., the zapper item which was a NES Zapper and the collector's edition pet, they usually will just change the sprite up and change the name.
But given how they still have the hero and plumbers items(vanity items that make you look like Link or Mario) still in despite Red's previous history of getting a cease and desist order from Nintendo over Super Mario X, I doubt they are going to remove the portal gun