BTech in Food Technology or B.Sc. in Food Technology or B.Sc Mircrobiology?
BTech is an engineering degree (applied science) while BSC is pure science.
An engineering degree gets a slight advantage over BSC, but provided you get good grades. If you are just average in engineering, but a top ranker in BSc, obviously you will have better chances of getting a top job with your BSc degree more than an average engineering degree.
A good way to choose either is to know that engineering is more technical and thus has a more tougher syllabus compared to similar BSc degree. Hence, the choice need to be made on which one suits you more.
BSc. with MSc is a very good option, if you feel B.Tech would be a bit tough.
A good comparison of BSc and Btech is provided in this link here – http://genwis.com/engineering-science/bsc-or-btech
As to scope of food tech versus microbioloy – food tech is comparatively newer than microbiology field and hence microbiology has an upperhand when it comes to getting a job quicker in research labs etc.,
In the long run however, both are equally good, provided you do your higher studies and get in to good grades.