How can I make this sentence unambiguous?

Such questions are usually hyphenated as thought-provoking questions, and if you're going to delete elements in conjoined multiple consecutive xxx-provoking usages like this, standard practice is to at least repeat the hyphen...

I encourage thought- and discussion-provoking questions by students.

Personally I would not advise reversing the order of thought and discussion here. The far stronger associations of the idiomatically commonplace usage linked to above can easily survive being interrupted by and discussion-, but discussion-provoking questions is relatively speaking such a rare collocation it would end up being "drowned out" (particularly if we consider the spoken context, where no-one can hear the hyphen that's supposed to resolve the very ambiguity OP seeks to avoid).

EDIT: Noting @jxh's comment below (it seems odd to invent such a usage), and the fact that @Janus's "supporting" example involves compounds which wouldn't normally be hyphenated anyway, here's a link to CMOS (Chicago Manual of Style) endorsing a group of eight- to ten-year-olds, which I think is essentially the same construction. (i.e. - I didn't "invent" it).

I would use thought-provoking, so I would interchange discussion and thought:

I encourage discussion and thought-provoking questions by students.

You are trying to imply discussion-provoking, which isn't idiomatic and is causing the confusion.

My suggestion is intentionally ambiguous, because I personally feel students should be permitted to initiate a discussion free from the constraint of needing to phrase it in the form of a question. If you insist that only questions are allowed to be the initiators of discussion, then I would reword:

I encourage students to ask thought-provoking questions that promote discussion.

One of the key requirements stated by the OP was that he/she wanted to encourage questions that provoked both thought and discussion. Unfortunately, there is no existing punctuation to enforce this requirement. In printed form we can bolden the words, as I have here and emphasise them in speech, but this is not really punctuation. In practice, we have to use the word 'both' to convey this fact. I would suggest:

I encourage questions by students that provoke both thought and discussion.

Why not simply rearrange the order?

I encourage questions by students, provoking thought and discussion.