Although it doesn't make religion right or sensible, but the argument that "religion has played an important, if not key, part in bad things that have happenned, therefore all religion should be rejected" is a poor application of logical reasoning
Who said this?
And, actually, religion has played a VERY key part in many, many, many bad things that have happened. It still does today. This we know. Why would you try to minimise that?
Anyway, my main reason for rejecting religion is that it is quite clearly not true.
It doesn't change my argument against the position that just because it is random it therefore can't have a cause, just not one of which we have knowledge
But that is no argument at all - and I said the same thing myself 
Bear in mind we are discussing Craig and his "proof" of god...Kalam.
Everything that begins to exist has a cause
The universe began to exist
The universe therefore had a cause
We call this cause God
I am sincerely astounded that anyone with any passing knowledge of physics would attempt to give this headroom. The problems with it are multiple...not least of which is the flawed opening premise.
Things happen on the quantum level of the universe that are counter intuitive and at odds with our everyday experience. This is what makes it all so very mysterious. You know this, right?
One of those mysterious things are virtual particles that pop in and out of existence at random, cannot be studied because they are not around long enough, can only be observed indirectly and cannot be predicted. It would APPEAR, on current evidence, that there is no cause.
You are doing exactly what the Christians are...assuming there must be a cause because up here we don't experience uncaused events. But you seem to be missing the fact that we're talking about quantum mechanics which seemingly bear little relationship to our own experiences of how things work.
There may be a cause...but because we are in the counter intuitive quantum realm there EQUALLY may not.
Therefore, Craig is beginning with a flawed premise. GIGO...you know what that means, I'm sure, being a physicist.
This, of course, is quite apart from the overall deductive reasoning, special pleading and necessary discussion about how we are defining "universe".