If it's very comprehensive and well tested, then I don't see any reason you can't market it as a standalone file, as long as you can work around some of the limitations the compiled runtimes have.
A better solution would be to actually get an SBA license, and roll the $100/license cost of filemaker into the cost of selling it to people. That way you could unleash all the features, and still lock down what you need to. Although you'd probably want to upgrade to v.12 instead of sticking with 11 long-term. The SBA and FBA programs give you good contacts with Filemaker as well.
Another solution would be to deploy your solution in a SAAS environment, where your clients log in to filemaker "terminals" that are set to auto-run your solution on-login. I know worldcloud.com provides this service.
Lastly, as you suggested, a web version could be a good way to go, but possibly expensive. You might want to wait a bit to see what plans Filemaker has for improving IWP, they might make some announcements at Devcon coming up in a few months. There might be a viable option for you to deploy filemaker web publishing after you convert your solution up.
Honestly without knowing / seeing your product, any of the above methods have both ups and downs.