Hey I think you should go into the MMA programme its better to do that and build up your skills all steadily rather than stick to one thing. If you just do BJJ you will get a major shock first time you get a head kick lol and likewise if you just do Muay Thai you wont have a clue how to defend submissions. Make sure you ask your MMA instructor what they cover because a lot of MMA classes are sometimes just teaching you all the techniques not as good as you would learn doing the single martial art.
Do you have any previous experience in any martial art?
Good luck with whatever you choose.