You are correct; it is not a sin to be born with a deformity. (See John 9:1-41, where Jesus talks about the man born blind.)
My reason for citing Deuteronomy 23:1 was more along this line of reasoning:
It would seem that, if a man had the choice of entering the assembly of the LORD or doing something that would prohibit him from entering the assembly of the LORD, then he should choose to enter the assembly of the LORD rather than doing that which would prohibit him from entering the assembly of the LORD.
Applying this principle to Deuteronomy 23:1, it would seem that, if a man had the choice of keeping his reproductive system intact and functioning normally or deliberately doing something, like getting a vasectomy, that damages his reproductive system so that it no longer functions normally, then he should choose to keep his reproductive system intact and functioning normally rather than deliberately doing something, like getting a vasectomy, that damages his reproductive system so that it no longer functions normally.