I do not know if this will break in the future, but it can. To minimize the risk, you can try to do a unit test of your injection routines, so when you make changes, you will have a mechanism to ensure that your injection routines will still work.
As a rule, I think that consistency improves quality, so I would consider code refactoring to use one provider. I use Ninject and I have 4 modules for injecting services and repositories. Each module contains 10-20 injection procedures - I can reorganize them within an hour. If your project is the same size, then refactoring and using the same IoC.
Edit I have never used ServiceStack.Net, but how much is your project dependent on this structure / toolkit? Most likely, in the near future you will replace it with something else? How much does this depend on your MVC project? I am trying to think of a scenario where the maintenance costs of using one IoC will be higher than the maintenance costs of using another IoC.
Looking at Ninject, there is an extension Ninject and Ninject MVC 3. The extension simplifies the work and does not conflict with anything else. In my case, I had to replace the standard Ninject with Ninject MVC 3, because for me it did everything that the standard version did (+ optional), and it was easier to configure.
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