If the package is cheaper than flight only then i would opt for the package. I dont see why this would be a problem regarding the return flight - just make sure you ring the airline and tell them you wont be needing the return seats.
The only problem i can see is the visa, but as you have already stated, you will be sorting this out before you go.

So, yes you can book the package
have fun
nicola

One small word of warning. If you fly into India on a charter flight you are meant to return on one and not use a scheduled airline.
In 2003 we had a mix-up on our return ticket. We had a ticket in our hand for a return on Monach but were not on the flight list out of Goa and the flight was full. Initially the airlines wanted £750 each person one way to fly us back. It took a day and evening of phoning to get transfered to a flight home free. In the end our travel agent managed to get us transfered to an Air 2000 flight.
We had tried to confirm our flight 72 hours in advance when we found out about the problem so atleast we still had our accomodation. Obviously this problem would not occure if you are travelling with a tour operator as the would sort it, but we found no one in Goa wanted to know.