"Known atheist"
What are we, terrorists now?
To answer the OP. Two people within the same religion is no guarantee that the relationship will work out. People aren't as easily defined by any single philosophy they hold. I would say that the answer depends entirely on the couple in question. You both should know each other quite well before going far in your relationship and be aware of each other's limits and respect those limits. No two people are perfectly meant for each other and relationships take work.
It sounds like you two are already at that point so I will simply wish you guys the best in your relationship and don't listen to what the nay-sayers have to say. They always have something to say.