I am working in an Islamic company. They allowed us to offer salaah either in a Mosque near us or in the office premises. The Mosque near us is of Hanafi School of Thoughts, so I was happy to offer salaah in our office premises. Now they instructed us that I have to offer Salaah in this Mosque only. So, my question is that should I offer my salaah in mosque with congregation or I should perform it myself?

You should have prayed with the Jama'ah in the Masjid instead of by yourself in the office.

Ibn 'Umar (رضى الله عنهما) reported, the Messenger of Allah (ﷺ) said,

"Salaah in congregation is twenty-seven times more meritorious than a Salaah performed individually." [1]

Hanafis are Muslims and we can and should pray behind Muslims. If they are practicing some innovations (bid`ah) before or after the Salaah, don't join them in their bid`ah, but join them in Salaah.

Reference:

[1] [Al- Bukhari and Muslim]