True, but the MoD and GoI are hardly going to want to go against the wishes of the military in such a manner. They have held a consistent line of giving the military what they want/need and they have stated they want to improve military-civlian relations- the IAF had made a compelling case for the Rafale and nothing else and the Def/Fin Minister (Jaitley) was said to be pleased with the finical side of the deal so I don't see any reason the MoD/GoI would go against these recommendations.
They can't go for IAFs "wishes" they have to take IAF's "suggestions" seriously and according their requirements and trials, as well as the commercial offer, the Rafale was the best choice (
till 2012!!!) and not because IAF just wished to have the Rafale.
The government has to consider what the best for India would be and not only for IAF, this includes industrial advantage or political once too. We know that the older government had kept out political influence completelly out of the MMRCA decisions, just as their priority was on ToT/offsets for Indian industry.
We DON'T know what the new government has in mind so far and what Mr Jaitley says at the moment might have more importance from the point of view of the finance ministry, since he is only a stop gap defence minister. Personally, I think Modi has taken this decision to use him in front of the media, while taking decisions with the forces (maybe industry or foreign governments) on his own. He is bypassing ministers in other areas as well and a propper DM in charge now, could be difficult for him, but that's another topic.
Wrt MMRCA, I showed you why MoD/GoI could (imo even should) re-evaluate things, of the 2 shortlisted fighters. The 2 year delays which causes changes in the delivery time frame and the technical changes must be taken into consideration, to get the best package of advantages for India. Not to mention, that although the Rafale is still the best fighter for IAF, the French disappointed in the recent time, by showing that they keep seeing India only as an export customer, rather than seeing us a propper strategic partner for the Rafale.