Fear in combat is a very real thing! How a person deals with it is what defines bravery! I like the fear system because, all too often, I see players willing to march headlong into the greatest horrors of the universe with a snarky "I don't care! I'll just roll another one just like it" attitude. The fear chart to me is not nearly as debilitating as you make it sound! On top of that, there are very few creatures in the RAW that actually have fear as a trait. Remember that the 40k universe is in a large part, a gothic horror game! If players encounter an extradimensional creature of hellish appearance who's reason for existence is to rend from them their very soul, maybe they should be a little fearful!
This also means that "Jaded" Characters are that way for a reason! Remember, any character with 20 or more insanity points effectively also has the "jaded " talent!
I don't think that certain abilities to ignore fear in the system are an issue. Most of them happen in an incremental fashion! Fearless for example, is a tier 3 talent that requires a Tier 2 talent (Nerves of steel) in order to buy. Yes ultimately, The fearless talent does allow you to ignore fear but you'll work to get there.
Lastly, The majority of effects below 100 on the shock chart are either temporary or allow for the character to "snap out of it" on any result below one hundred. Unless your players are all phenomenally bad die rollers (or doing it deliberately) I find it hard to believe that a single shock test (Especially at fear levels 1 or 2) would cripple half the squad!