Simply put it, if there was no Pakistan, there would have been no Bangladesh. Talking about alternate realities is a complete waste of time.
There are various books that are part of secondary school curriculum in Bangladesh. Of-course, they were approved by the ruling BAL. They do mention and support the two-nation theory by stating details of how Muslim-Bengalis wanted a Pakistan to avoid "Hindu-domination". Suffice it to say, Mujib did support the two-nation theory.
The West Pakistani leadership did not accurately acknowledge the security matters in East Pakistan. Especially after instigating an insurgency in north east India during the 60's. East Pakistanis alternatively thought that a new nation "Bangladesh" can manage its own security. Part of why they wanted to break away.
Now as far as these present "Bengali-nationalists" go, yeah they are a bit of a mental case. As stated here by an AL supporter:
http://www.defence.pk/forums/members-club/282704-bible-scholar-makes-explosive-allegation-about-jesus-9.html#post4869156
It appears that these conspiracy theories about AL loyalists being anti-Muslim may indeed be true. How it is so remains to be seen. Seeing how Bangladeshis generals can get slaughtered by their own soldiers, and this^, security is still a far away dream.