Hmm, I don't know much Farsi (but I can sound it out), the billboard in the article doesn't say anything about Khamenei, Google translates it as "free gas at the Jamaran gas station"... I'd think the Times would have someone on staff who could have checked that.
Any way you look at it, Times of Israel is not exactly an impartial source on current affairs in Iran!
Your translation is correct. This billboard is a reference to the home of former ayatollah Khomeini. Regardless, the hackers are trying to point the finger at the clerics.