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.

If you are talking about more than two stories, your colleague, I think, is right. You should use the superlative longest for more than two stories as follows:

Which story was the longest?

However, if you are talking about comparison between two stories, your colleague isn't right. 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".

Besides, the use of the superlative for two things or persons is more common in informal English.