One more option is to book ticket to Delhi or any metro city in India and book a separate ticket to Pune. This would definitely open up many options and you can adjust timing and book ticket to Pune. If you want all the way, Air India is the best option looks like with good connection and lay over timings.
With the Indian domestic baggage limits and charges for excess baggage, separate ticket will work only if OP is traveling really light (<= 15 KG / 33 LB per person). This also provides no safety from missed connection.