Okay, this does not seem to be anything to worry about, and you can get around it with ease.
Presumably, you are currently pointing Inner Space at eve.exe (this is currently default from Inner Space) or launcher.exe.
If you point Inner Space, instead, at EVE\bin\ExeFile.exe -- this is the actual game client -- the game will NOT bring up the launcher.
You can modify an existing Game Profile with the different executable, like so:
1. Right click Inner Space in the system notification area and select Configuration
2. Click the Game Configuration tab
3. Select the Game in the first drop-down box
4. Select the Game Profile in the second drop-down box
5. Adjust the Main executable path -- because eve.exe is not in the same folder as ExeFile.exe. It needs "\bin" at the end, like if it's currently C:\Program Files (x86)\CCP\EVE it should be changed to C:\Program Files (x86)\CCP\EVE\bin.
6. Adjust the Main executable to be ExeFile.exe
7. Click Apply
I'll also release an IS update soon to fix the issue it has with the launcher.