I completely understand your fear--I am the same way. Exposing my nose to water just makes me uncomfortable. But don't worry, like others said, you WILL get used to it. Just take it slowly. When I got certified way back, flooding my mask was not part of the training, at least not during the open water checkout dives. Then I didn't dive for a number of years, and when I finally got back into it, I accompanied my then girlfriend during her certification dives, just for fun. When the instructor had everyone sit in a circle at 30 feet in the ocean and do the mask flooding exercise, I thought to myself, "He's got to be kidding." But I forced myself to do it, along with the students. As soon as I got back into diving more regularly, I practiced flooding my mask and removing it quite frequently. The frequent practice brought me to a point now where I comfortably can switch masks at depth. All it takes is collecting myself, preparing mentally and doing it slowly and consciously. I find it helpful to do it step by step: Flood mask first, but don't take it off yet. As soon as you feel everything is ok, slowly remove it and continue breathing through your reg, slowly and easily. Exhale slightly through your nose if you want to prevent water from entering. I always remind myself that even in the event that I breathe in a few drops of sea water, I can cough through my reg and still get all the air I need. Trust me, the discomfort you experience is only natural, we mammals have an inbuilt urge to close off our airways when immersed, but with practice and time it won't bother you at all. Part of it may also be that if you're a nose breather (I know I am), it takes a little more conscious effort to suppress the urge of inhaling through the nose. That's where the practice and doing it slowly and consciously come in.
No worries, you'll get there!