I have an issue with one of my teachers and a chance to address it, but they're writing me a letter of rec. Should I address it?
What I wrote is strongly worded but I feel like it gives a fair assessment of what my problem was.


I would reconsider the strongly-worded part. Giving a fair assessment is good, but people rarely react well to sharp criticism, and this can burn bridges. My advice is to state facts, not conclusions. For example, rather than saying that you were "discouraged from intellectual exploration" (a conclusion), you could say that you were "disappointed not to be able to pursue X" (a fact). 


  Should I include my assessment or should I hold off until after I apply?


Assuming what you write is not ridiculously far over the line, I would not expect your professor to change their letter of recommendation. Particularly if they've already written it, I doubt they would take the time to go back and make changes. 

But, consider the cost-benefit analysis. The (potential) cost is burning a bridge (you can mitigate this by being diplomatic). The potential reward  is that future students might have a better experience, but this is likely only if the professor (a) does not already agree with you, (b) agrees with you after reading your report, and (c) chooses to address your feedback.