I'd really recommend reaching out to Squad or maybe even Unity to see how things are done in KSP. They have a really vibrant modding scene over there- the obvious use for KSP mods, adding new engines, fuel tanks and stuff, is obviously front and center. But there are mods there to set up communication networks (and unmanned crafts can only be controlled when they can reach your comms network), resource prospecting, mining, and refining into fuel, a completely rewritten aerodynamics system, all kinds of great stuff. And I get the impression that the level of work involved on Squad's end is very low because they use Unity's existing event piping systems to alert mods to stimulus.
Essentially, that's all we need- currently ACTING ON the server is usually possible (but some help here in the forms I detailed above would be great), if via nothing else but reflection. The biggest obstacle for modding currently, what tends to call for IL injection, is the difficulty of allowing the game to provide feedback to the mod. The only way of doing so currently without IL injection is console commands, and even that poses an issue because only one mod may override the chat class at a time currently.
In theory, if you injected your IL to the dlls then I ran the Oxide patcher on your edited dlls, both mods will work concurrently without any issues.