These roommate situations can always get a little sticky. In principal, I don't think there's anything wrong with reducing the rent-split for a person who has a smaller room, or in this case splitting the room. When I lived with roommates, I always took the smaller room available and my roommates in every case agreed to let me pay a little less. The question is how much is fair? In my experience the discount was about 15%-20%. If your roommate expects to just split his half of the rent with his girlfriend, then I would say that's unfair. She still gets equal access to the living space, the kitchen, the bathroom. And I think it's only fair to equally split utilities.
The reasoning your roommate used to justify cheaper rent, "she won't even be around the house that much, compared to you," sounds like a bunch of BS to me. He's suggesting that somehow the amount of rent one should pay is based on how often they're home. And that's just not how it works. I'm sure when you sat down with the landlord to negotiate the lease, if you tried suggesting, "Hey I plan on only spending about 80% of my time in the apartment, can I pay only 80% of the rent you're asking," this would not even be considered, and probably laughed at.
What happens if his girlfriend ends up spending more time at home than anticipated? Do you get to raise her rent? Why is this the deal just for her? What if you get a new job and start commuting and spending less time at home, do you get to lower your rent? What if you go on vacation? Do you get to not pay rent for the time you're away? Universalize this principal. What if everyone kept a log of the time they've spent in the apartment and then paid the appropriate portion of rent? Of course that would be impractical.
It seems to me that your roommate lacks empathy for you in this position. He really wants to live with his girlfriend, which is understandable, but doesn't consider how this affects you at all. I've been the guy with the girlfriend in this situation. I talked about it with my roommate at the time and I understood he wouldn't be comfortable with the arrangement. I never forced it on him and we continued to get along just fine. My solution ultimately was to move out to a new apartment with my girlfriend.
That being said, it could end up being a great arrangement and you'll get to pay a little less in rent. But don't let yourself get bullied into something you're just not comfortable with. Once she moves in, she'll likely be there to stay and you might be the one getting pushed out.