It depends on who your partner is. Some people are more reasonable than others. If he or she is the type of person that can see the logic in your position and understands that there needs to be 1 person who can ultimately make decisions, then it will work.
But, if they're hard headed, then you're kind of screwed. I would suggest that you offer them something in return for giving up that 1%, like a slightly higher salary if/when your company starts generating money.
Owning shares in the company is more important than a salary anyways but most people don't realize that in the early stages since the company isn't worth much if anything.
For instance, Facebook gave an artist some shares in the company in return for a painting that he did in their office; this was like the very beginning stages of Facebook when they were just a college social network.
Anyways, those shares ended up getting that artist hundreds of millions of dollars when Facebook IPOed. Clearly, people treat company stock like toilet paper when it's just getting started out.