There's a difference between ripoff and homage. In fact, the credits do make note that Barney's Mind was endorsed by Ross Scott. Also, in canon, Gordon Freeman and Barney Calhoun were actually friends at Black Mesa. Alyx made note of their competition as to who could get Kleiner into his office first when he lost his keys.
When I was making my minds series ("Kane's Mind," based on Quake 4) I tried to tip my hat to those who came before me. And yeah, I accidentally ripped off one of Ian Riley's jokes with Kane's line: "Are you dead? Stop being dead!" The original came from Riley's "Harrison's Mind," where the line was "Are you dead? Why are you dead?!" I totally forgot until a couple of days after I published it.
I compare the Minds series like I would compare the actors portraying James Bond. Ross Scott is like Connery...the original, setting the standard, and a high one at that. Ian Riley is kinda like Daniel Craig...at first glance you don't expect him to meet the standard, and then you actually see him in action and he manages to pull it off.
Seriously, the "Master Minds" actually pull off some quality work and create their own flavor. (Actually I think Ross Scott has a standing invitation to that group...either that or he's considered not so much a Master Mind as he is an Uber Mind.)