It just makes it a little harder to make money for Free! Winning a ticket first and then using that ticket to play in another Tournament is just another way of getting more value from the game for PokerStars.
If they offer $100 Freeroll and the top 50, 60 or 100 players get into the Money bubble, They are all making money although for some it might only be a few Cents, but they can use that to buy into other games once they amass enough Micro wins, But if they offer $100 Freeroll for Tickets then only 20 players could possibly win a $5 ticket each, they are then limited to playing in the next Tournament that is on offer, So in effect they have no choice but to play that game.
Sounds like a good business Plan for them to make changes that make them more money, Let's be honest they are in this to make money, Not give it Away for Free!