I know it may disappoint you, but much of what you have stated is frankly not true. No Muslim goes about "blurting Vande Mataram", except for those who seek political office allied to the BJP.
Secondly, the Deoband scholars in India, are well respected around the world, even by Pakistani deoband scholars. They may have some conservative beliefs that you may be uncomfortable with, but they well within the scope of Islam.
Third, and most importantly, you base your thoughts on an article printed by The Print, a notorious anti-Muslim rag that puts Radio Rwanda to shame. I would bet 100% the author posed some idiotic questions and the answers from the people at Deoband did not even match what the author wrote. I recall somewhere else that the Deoband scholars simply said that "we are from India and have nothing to do with the Taliban and they are free to do whatever they want in their country". Note how such words were rehashed.
This is the India of today, where Muslims are repeated questioned about Muslims from all around the world, simply to evoke some controversy. Until a few years ago, it was the favorite past time of the so called journalists in India to go to Deoband, and ask for some fatwa on some stupid issue. Then those words would be twisted and published all around India with a triumphant note showing how regressive Muslims are. Deoband put an end to that by stopping the issuing of fatwas to the general public and now every fatwa is approved by a committee and posted on their website.
Another note - Self-preservation is a natural reaction when it comes to living as a minority. In a hostile country like India, those tendencies are magnified. What you may interpret as "pandering to the Hindus" or "not Muslim enough" is actually self-preservation. The more important mission here is to educate the coming generations about Islam. That is more important than engaging in hostility with the majority just to soothe the egos of a few people west of the country.