Am I protected if I use the word "alleged" in crime stories?

Only if you attribute the statement to an official source that you are privileged to report. If you opt to use the verb "allege" in a crime story, the subject of the sentence should be "police," "the law suit," "an indictment" or some other official source, which is then fairly and accurately reported. Keep in mind that reliance on an official documentary source over informal disclosures by officials is always best.