Personally, I think any theist who is offended by an atheist referring to God as an "imaginary friend" is a very weak theist, indeed.
There are instances on TOL where offense is intended (a good example is the reference to a "flying spaghetti monster" nonsense that so often gets posted) and those should be reprimanded because they are stupid and intended only to offend. But referring to God as an imaginary friend is not one of these. I am a theist and a Christian and I understand full well that God is a fundamental and divine mystery to we humans, that we conceptualize in various ways, each according to our needs, or history, and our own nature. For a great many theists God IS an "imaginary friend". And there's nothing wrong or insulting about that. In fact, it's just one of many healing attributes of having a belief and faith in God. No theist should be ashamed to admit that their idea of God is "imagined". One, because it's true. And two, because it's part of how the healing works. God is an object or faith, not a matter of fact.
Not only that, it makes the theists of TOL look weak, and petty, and intellectually childish to be banning non-theists for what is essentially an accurate characterization of their conception of God, even though it is a very limited and naive one on the part of the atheist. And I don't doubt that in the atheist's mind, characterizing theist as "imaginary" could be intended to belittle, as some atheists believe that imagination is somehow wrong, deceptive, childish, or otherwise unimportant; which is ridiculous. I also know that stuu can be somewhat abrasive in exactly this way.
But I think the OP is right. Atheists do believe that all gods are imaginary. And they can't be expected not to say so. And theists make themselves look petty objecting to it when in fact there is some truth to it. Even if not in the way that the atheists think.
Frankly, we theists ought to be stronger and more honest than this. Especially in how we present ourselves to the non-theists.