I only deep throat my husband once in a while, and although it doesn't really bother me it isn't my favorite thing to do. If I'm getting tired or just don't want his whole cock in my mouth I just use my hand also. So long as you keep your hand pressed next to your lips and create a kind of seal between them, the guy really won't notice much difference and it is much more comfortable. Plus you can do fun twisting motions with your hand at the same time, my man loves this.
And to echo Essin' Em, you should only do it if you want to. Oral sex is a gift that is given, not forced, even verbally. Forced oral sex is rape just as forced or coerced intercourse is rape.