If you're concerned about them modifying or redistributing the code without your permission (I assume that's why you want to retain/obfuscate the source), then the most effective way to achieve that is also fairly simple: Hire a lawyer to write a license which specifies your desired restrictions.

Any obfuscation you may do to the source can be undone, usually fairly easily. If you can compile it to native code, that would raise the bar by requiring disassembly, but that's still doable - and, if you don't have that license in place, they're probably within their legal rights to do it. (Or maybe not... I'm not entirely sure how DMCA would affect the situation in the absence of a license agreement. But, then, why take that chance if it's a concern?)

They need to be able to access the code, in some form, to be able to run it and if they have access, they have access. The only way around that is to run it on your own server (possibly located at their site, so it can be part of their intranet) which they can only access via your code's web interface.