As a student, you simply need to go along with your supervisor's recommendations. You are not in a position to dictate the terms. Using the proprietary tools will not hurt you, unless you need to buy your own. If it were the case that you needed to buy your own, then I would ask your supervisor for another solution.
Even as a Junior faculty member, you may be in close collaboration with other faculty and should follow the consensus. That is how you work with other people effectively. You don't keep asserting that your solution is better. When you are calling the shots, you can use the tools you wish.
So, you need to adjust your attitude. It may be that you are presenting the issue of principles - I prefer free, you prefer proprietary, but that is not really the true issue. Maybe you don't know the proprietary tools and don't want to learn them or feel you can't learn them. Choice of tools you use is no reason to switch graduate programs.
This is entirely a matter of getting along with other people, not being selfish, etc. These are life skills we are talking about.
Kevin Buchs