This is an intriguing problem. I think, by RAW, you've got the long and short of it, and if that's sufficient for your play group then I would simply agree that the attack is wasted.
However, rolling "too well" is terrible and unintuitive from a game mechanics point of view. (This is different from accidental overkill in that there is no actual effect to apply, rather than a dramatic effect which may be directly punitive towards the attacking player, such as catastrophic damage and so on). As a result, I would suggest employing some house-rules to prevent this from happening. In general, my attitude towards game mechanics tells me that all "results" better than the minimum possible threshold should have
some mechanical effect - in other words, only failed rolls may "fizzle."
In this particular case, I would suggest treating the 5-6 result on the Space Hulk Crits table as a 5+ result instead. This is the simplest way to fix the problem and still have an actual effect for game purposes.
(BTW, thanks for asking this question... I hadn't thought of this issue and was able to make a fix for my rules project as a result
)