If you use the pronoun to talk about more than two things, your colleague, I think, is right. You cannot use the comparative longer for more than two persons or things. You should use the superlative longest as follows:
Which story was the longest?
However, when you talk about comparison between two things (two stories), you can use either the comparative longer or the superlative longest. So both the following sentences are correct:
Which story is (the) longer?
Which story is the longest?
You usually use the superlative with "the". But sometimes you use it without " the".
Please note that the use of comparative for two things is a bit literary or formal, but the use of the superlative is informal.