I believe the answer to that is "absolutely". They certainly weren't in it for the money at first. Woz had to be very explicitly convinced to leave his nice job at H-P even after they had built the first Apple PC.
If you insist that their friendship was somehow bogus because real friendships do not involve "shared purpose", I'm not sure I have any friends, by your weird definition. My high school friends had the shared purpose of playing games and entering math contests. My college friends had the shared purpose of graduating.
I'm working with some great folks now and we simply started by trying to build something. We're still in that mindset. We didn't start out as friends but after eight months, we are. There's the pressure to get stuff done because we don't want to let each other down. We laugh more than we disagree. It feels like the friendships and the startup are growing together. I have a hard time thinking that the team could be flawed because we didn't start out knowing each other well.
They may not have been friends when they started collaborating on their first research project, but at the moment they were "co-founders", they had already become friends.
Shared trials make and break friendships.
That example of Viaweb helps clarify the distinction I'm thinking of. You guys were friends and so worked together despite differing convictions. But what of people who share a common purpose and in so doing become friends? Is there room in your model for that instance of the concept?