How do instructors grade a one-person project when everyone else in the class worked in pairs?
First, I'm surprised the instructor didn't ask for a volunteer to work alone. In a reasonably-sized class with pair projects, there's almost always at least one student who would rather not work in groups or pairs.  It seems a lot of this angst might have been avoided had the professor simply polled for a volunteer. Is it too late to ask for groups to be rearranged? He could ask for a volunteer, and you could be paired up with that person's previous partner. 

(Then again, maybe those students who would rather work alone are the very students who need group experience the most – and maybe that's why your professor opted to do this at random.)

Getting to the crux of your question, though, I would first study the assignment carefully and imagine how things might be different if you were working in a team of two. Would you be able to divide up the work? Brainstorm ideas? Once you have something concrete in mind, I'd reengage with the professor and ask for more clarification about how you will be graded. 

In other words, if you simply say, "Will I be graded more leniently?" that might be regarded as premature grade grubbing. However, if you say something more specific, like:


  I noticed this project has a lot of work, and I think I might be at a disadvantage working alone instead of in a team. For example, if I had a partner, we might divide this up, so that he was working on the interface while I was writing the guts of the program. If I have trouble getting this assignment completed on-time, will you take into account the fact that I had to work alone?


then I think you'll get your professor to think objectively about your disadvantage and answer accordingly.

It's generally best to be up-front about potential hardships that might affect the quality of your work, and to do so early. Otherwise, you risk coming across as a whining procrastinator. However, your question is reasonable, and I think it's best to get an answer sooner rather than later.