Can't you tell your boss that you've already accepted an intern offer? Emphasis how important it would be to your thesis work.

If he still says no, then you have to break up your promise to the company, no choice.

Maybe your boss would give up...

我当年也为了取悦老板，放弃intern（before landing an offer), 现在想很不值。实际上，我如果去了intern,会对我后来research很有好处。相反呆在实验室白白浪费了三个月，没干出什莫。假如我那会把这个理由跟老板说了，他肯定支持。

For both questions, it differs from scool to school. Check with the office which issues CPT in your school if you need any reference letter from your advisor as a PHD student (for summer intern, usually it does not).

But you'd better get your advisor's agreement anyway. Persuad him that how much your research ability would benifit from this oppotunity. For example, for later research work, you would be able to finish in 3 month rather than 6 month given the experience you would collect from the internship. Suggest someone else to do the work he wants for the summer. Make it clear that you very much want to do the intern--he probably would not like to 'break up' with you as much as you do not want to break up with him. Do the negotiation, politely. Even if he insists you working in lab at last, DO NOT get emotional--just give up the intern.