Let's dig a little deeper in the whole issue rather than making judgement from a couple of articles.
As soon as CSA posted the itinerary for India's tour of South Africa, BCCI objected straight away because it included 3 tests which is good but 7 ODI's. Are you kidding me, 7 officialing ODI's? And 2 T20's.
India in South Africa 2013-14 : BCCI objects to South Africa tour itinerary | Cricket News | South Africa v India | ESPN Cricinfo
Now if you remember, India travelled to South Africa in 2012 just to play a meaningless T20 match.That match was held as a tribute for Kalis. That match was not scheduled in the FTP but those Indian players still travelled all the way to South Africa just to play one meaningless T20. Does that mean BCCI is CSA's puppet or those players are puppets who were used just to make that tribute match happen for Kalis?
It's not like they have forced the WI players to come to India. If WI board denied this offer, BCCI would have called some other team over because they want to lay a perfect platform for Sachin to retire in his home ground. Obviously he deserves that after what he has done for India and the game of cricket in last 2 decades. So Sachin is not above the game but what he has done for the country is enough to give him this opportunity to achieve this milestone in his home ground or country.
Again, the first question you asked can be true because BCCI has often violated FTP so it's nothing new but this time it is for good. And it is very likely that South Africa tour will be down to 2 tests, 3 ODI's and a T20. BCCI and CSA has been very friendly towards each other since South Africa's readmission into International cricket but this recent appointment of Haroon Lorgat as a CSA chief is causing all this issues between the boards.