That may be how things work in some countries, but not in the US, even under Trump.
Let’s Encrypt evidently didn’t mean to block all of Iran, only the Iranian government, which I assume is capable of getting its own certificates: https://news.ycombinator.com/item?id=48465754
Let's Encrypt evidently meant what they said, and the evidence is the fact that they said it. And they said they were sanctioning the whole country of Iran.
Why did you think Let's Encrypt suddenly blocked Iran? It isn't because their board members have the same ideological alignment.