How to support a student whose aspirations I don't support?
I don’t really understand what part of your “support” your question is about. In short: is the problem how to support him personally (in your discussions with him, in your work relations in general), or how to support his PhD work, or how to support his job application?

For his PhD work, I hope you are able to prevent outside circumstances from impacting negatively your work. As an advisor, this probably happens at some point with any student… and  any coworker, really.

For his job application, you don't need to state to support his future job, just to say he would be excellent at it. Just to give an example, stating that “Dr. Martin has all the skills necessary to excel in numerical simulations of deep offshore oil drilling” doesn't require you have to state “I strongly support offshore drilling”, nor does it imply it. Moreover, most recommendations are done in written.

Finally, regarding overall personal support throughout his graduate studies: that's a bit harder, but you truly have to put it past you, and it may not be easy. The best approach is clearly to be upfront with him: discuss it, preferably in an informal manner (i.e. don't make it a big deal). Points that seem important to mention:


I have strong feelings about your future employer, and I think it is best that I am frank with you about it.
It shouldn't change our work relationship, and I don't expect it to. I continue to support you wholeheartedly.
If you think you notice a negative impact in the future, please come and discuss it with me, we'll work it out.


But honestly, it's not a nice situation to be in. I'm a bit surprised as to how what could gather so much distrust from you that you cannot simply separate it from your work.