ISRO needs material scientists but not directly chemists. But you can go for BARC after your Integrated MSc. For ISRO , you will have to complete your MTech in Material science then you can have a job at ISRO.

Integrated PhD from TIFR , JEST participating colleges will really shape your future well. There is no loss for integrated MSc since you will sit in TIFR/JEST after your MSc but if you join Integrated phD then you will get involved in research at the top research institute in India will build your aptitude of research more efficiently than the other.

**Its my thought process. It may differ. You should conduct a internet search about both the courses and then only take a decision.

I hope my answer helps. All the vey best for your future endeavors!