Add module dependency information in each node. And disable rule if that node is present in a node if the dependent module is disabled.

Create a new key in node called "dependencies" which will be an array of strings. Which will save module names on which it is dependent. And on module uninstall we will check if any node is dependent on that module and if any rule is active using that node than disable it.
Also add a validation that that a node is not present in a rule whose dependent module is not enabled.