Hi!

It is not advisable to compare B.Sc. microbiology and BHMS based on the state you want to study in. Where B.Sc. Microbiology is a 3-year undergraduate degree with specialization in the mentioned field and is research-oriented, BHMS is 5-year bachelor's in Homeopathic medicine, which allows you to practice as a Homeopathy doctor after completion of your degree.

If you have interest in alternate medicine and you want tot become a doctor, you should apply for BHMS. Your excellence in this field will depend on how well do you treat your patients.
On the other hand, if you want to opt for research or maybe you're inclined more towards food safety and related fields, you can go for Microbiology hons.

Best wishes!