It isn't completely clear from your post, but if you were thinking of doing this without telling your flatmate I would seriously reconsider - everybody has the right to feel safe and secure in their home if nowhere else and whilst in a flatshare situation there are always going to be people around now and again that one flatmate doesn't know, the difference here is that you don't know them either.
Can you lock the door to your flatmates room from the outside, so that punters can't access it? What about the bathroom and shower - will they be using the same one as your flatmate uses and keeps her possessions in? If she did come home mid-booking, have you thought about what you could say that won't scare or upset her even more?
You could probably give it a go and nothing would go wrong, but the consequences if it did could be a real disaster even leaving other peoples feelings out of it - is there maybe somebody with a room in Seeking/Offering that could help? Even a couple of daily/hourly rentals should give you a bit of elbow room and maybe allow for a hotel day
.