Yes, that's why i am trying to do. My original post was not very clear sorry.
In the best of world, I would just rewire the Infrared receiver of the TV to the Pi and call it a day. The problem is that the tv needs to be in Video mode and (as far as i know) the only way to enable it is via the remote control.
I could have two infrared receivers mapped to the same remote codes (One to the pi and one to the tv), but then i'm still having the issue of the green display popping up over the video every time a button on the remote is pressed.
The only option I can think of is having two different remotes (one to switch to video mode, the other one to control the Pi), however that's not an ideal solution, was hoping for something more elegant.