Which script/filter could be useful for such cases of intersected handles ?
There are scripts for this. Tunnify in mekkablue’s scripts (https://github.com/mekkablue/Glyphs-Scripts/tree/master/Paths)
In this particular case you will need an extra point, if you want to do this without loss.
The idea is to avoid manual insertion of nodes; as you may miss many of these cases unless you meticulously examine every segment of drawn paths.
So far the Tunnify script seems not to resolve it.
No it won’t, because the handles are too long to begin with. That is why I said you will need an additional point.
Tunnify helps often, but not always 
In this case, a simple fit curve will do. And perhaps repositioning the on-curve nodes, but it’s hard to tell because I cannot see the rest of the curves.
Also consider turning this into a corner point, and adding a corner component that takes care of the rounding.