They wouldn't look down on it but they would do one of two things. They would either scrutinize your application to figure out why you have 3 (in which case they may contact you because you didn't explain it) or they'll just throw it away and not even look at it.
Now, the other component becomes even if you were to explain it, what would you say? "Well my boss really can't write that well and I feel s/he may not give me the endorsement I'm looking for"? That doesn't quite fly.
You should do a couple of things in tandem. Firstly, call the school you're applying to and ask them what they would do if you submitted 3. Don't get into the details of why but ask. In the mean time, more actively prep your direct supervisor. Give them the support and examples they need to understand what's expected of them.
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