If the C# "equations" can be saved and exchanged between users, then there is certainly a security risk. A user could put malicious code in the equation, and have it do bad things on the machines of other users. Or a user could simply be tricked into entering a malicious "equation" (think of the old alt+F4 prank here).
Fortunately you can safely host untrusted code in a .NET sandbox. The general idea is that you create a separate AppDomain (with the AppDomain.CreateDomain method) that has only minimal permissions, and then load and run the user code there.
Loading dynamically generated assemblies into a separate AppDomain is a good idea anyway, because it allows you to unload them again.