Well, the most profitable alternative is to not offer site licenses. That is, make your customers pay for every copy they use. (If they're a big enough organization to consider buying organization-wide, then they're also big enough to afford paying for each license).
That option requires you to change the way you do business with large companies.
The other option (the one where you don't have to change the way you do business) is to use our floating license server, TurboFloat. It's not yet out -- it's coming soon. But a floating license server is basically a "mini activation server" that runs on the company's intra-net. You assign so many allowed activations for the TurboFloat Server for that company, and your software in that company requests a temporary "software lease" while an instance of your software is running.
So if you assign 20 activations to the TurboFloat server then that company will be able to run 20 instances of your software at any one time. They can install it on all the computers in the company, but they'll only be able to start 20 instances at a time.
As I said, TurboFloat is coming soon. We're pushing hard to get it out before October.