Do condoms and diaphragms interfere with energy work?

Not at all. In fact you really don't need to touch physically. I had
a most profound experience one time at an airport with a friend,
sitting back to back, just breathing together. The more subtly you
tune into the energetic sensations, the less physical stimulation is
the focus. Certainly a little film of latex isn't going to have much
of an effect. Of course, if you're being monogamous, then it's nice
not to have to use such things. If you are having multiple partners
then they are a must. Use common sense.

How do I embrace my sexual energy, without feeling guilty or stupid for even wanting to?

For me this is really about acceptance. We begin where we are. In
other words, if you can accept that you feel guilty or stupid, then
perhaps you can let some humor in. Humor implies playfulness, and
with playfulness is the acknowledgment that goals are illusory. You
don't have to change. Be yourself, just as you are. That's the place
to begin. Play around with it. Check it out. Be curious. Laugh at
your guilt. Laugh at your sexiness. Realize that in the larger
moment, this is all passing away.