Hi,
After some more wandering on the web, I found out that this question has been asked many times before (sometime even on this very website). Unfortunately, the threads I found did not carry any answer and some didn't even got any reply.
I also found a bug-report (that remain open for now, there is still hope) on this topic :
https://bugreports.qt-project.org/browse/QTBUG-17869
I also got a promising article that pretend the solution is actually there somewhere inside Qt since version 4.4 (although it might involve some dark magics). I couldn't understand very well how to do it but it is apparently possible :
http://blog.qt.digia.com/blog/2007/08/09/qt-invaded-by-aliens-the-end-of-all-flicker/
Lastly but not least, I RTFM at the documentation on the QSplitter (which I should have done in the first place I know, sorry) and found out that it is possible to simply prevent the widgets to be updated while the splitter is being used :
splitter->setOpaqueResize(false);
Myself I will stick with my original solution for now : using a single QGLWidget and draw twice inside it using 2 differents glViewport with some custom splitter controls.
...at the cost of performance sadly.
PS : if you are looking for a solution on your own, I share that I had the best luck with the search engines using the following terms : qt, QGLWidget, flicker, resizing.