I have faced this dilemma too. We have been travelling with our pets (boxers, attached photos) for almost two decades and have faced the problem - pet accommodation - on many occasions.
Most of the time the situation has been resolved by taking refuge in the various accommodations (PWD guest houses, circuit houses, forest dept rest houses etc) along the highway ( Mumbai>Lucknow-NH3 /// Lucknow>Uttaranchal-NH24,31 & some SHs too) provided for public servants. A little talk with the chowkidar, a little gentle persuasion in the form of cash tariff & usually it works - with the chowkidar offering to cook your meals for you too! We carry our pet's meals (during travels) so that its not such a serious issue.
One of the reasons we love the Kumaon region in Uttaranchal is because of the open door pet policy of the KMVN organization - (Kumaon Mandal Vikas Nigam, the state Tourist Dept.) - in all its hostelries in the district. Comfortable, clean rooms, with hot & cold running water (a must in this region, with temps plunging well below zero in winter!), attached toilets with breakfast & dinner included in the tariff. Plus the obligatory cable TV in each room. The rates are very reasonable (KMVN, Naukuchiatal, our home from home there) from our point of view (2500/- to 4000/- depending on the season).
Our problems started when we added Lucknow>Kolkata to our itinerary. So far we have not found a pet-friendly hotel on the route (NH2 from Allahabad to Kolkata) nor the usual standby of govt. accommodation along the highway. The first time our night halt was at Bodhgaya where I slept in the car with our pets while the others spent a comfortable night in a hotel bed!
Thereafter we have not taken the risk of taking our pets with us on this route.
So we shall be obliged for any information on pet-friendly accomodation pertaining to this route.