Him being in the room will be fine. Salmonella is a very minor risk with proper hygiene and handling practices. The only thing you might want to change is for you to take over all the reptile cleaning tasks or have her wear rubber gloves when cleaning the enclosure. Make sure she washes her hands well after handling him as well.
I don't know if you house your beardie on sand, but if you do I would suggest switching it out because if fecal matter dries out in it, the particles could become airborn. Normally, that probably wouldn't have any severe side effects for a healthy person if the viv is cleaned often enough, but pregnancy can do all kinds of strange things to the body and the immune system.
There is always the fact that NOT ALL REPTILES carry salmonella.
Proven Fact.
However, unless you have had your beardie tested, you will never know, so it is always wide to practice caution.
Salmonella can be fatal in people of exceptionally weakened immune systems, so be VERY VERY careful when dealing with beardie, and then touching your wife.
I haven't checked if it can be passed to the foetus, but if you are sensible, you won't even need to worry.