"Denying or affirming religion is the same action. By GGP asserting that the being in people's beliefs is "imaginary," it is denying not merely the reality, but the very possibility of it becoming reality."
No, it's calling them imaginary, as in false. I know everyone likes to pretend that in science, everything is tentatively true or reasonable until data comes in to explicitly support or deny it, but that's simply not true. In science, fanciful ideas with no predictive value do not receive respect, they are treated as false until shown otherwise. The null hypothesis and all that. If you claim that leprechauns cause tidal shifts, I will gladly tell you it's imaginary, despite having done no original research on the subject. If you claim a fanciful, capricious creature created the universe, I'll do the same. It's shorthand for, "that has no empirical support and seems more like speculation than serious academic thought".
"Denial of anything unknown, whether it is asserted by a theorist or a scientist, is denial of potential knowledge"
What does that even mean? Who is denying "potential knowledge"? Rational skepticism holds that you wait for the evidence. Go ahead, bring evidence, scientists are completely open to it! Do the work! Until then, your claims will be treated as putatively false, certainty in their falsehood increasing with how little they have to do with empirical research.
"Science, which posits that knowledge is unprovable absolutely, only deny assertions that observations deny. That which is unobservable can neither be denied nor affirmed by science."
The confusion here stems from mixing layman's terms and the philosophy of science. Let's say I claim that purple space creatures seeded life on earth. The way to state an objection in philosophy of science terms is this: such a claim is supported by no empirical observations, or if there are observations, they are of a questionable nature (as tends to be the case with fantastical claims). It also doesn't make any predictions, and is thus fruitless. It could be true. Any fantastic claim *could* be true, even when it conflicts with a mountain of data. It is for precisely this reason that you'd simply say, "that's imaginary" instead. It communicates the same idea - your claim (or my claim) is implausible, supported by nothing, is useless, and fits the pattern of imaginary things.
"Your GP isn't being critical, he's being intolerant and narrow-minded."
How so? They're being obviously critical, calling religious claims imaginary and stating that efforts could be better spent on other activities. How are they being intolerant?
tl;dr: science doesn't work like you think it does, it does not tentatively respect nonsense claims but treats them with the lack of respect they deserve. This can be pedantically stated as, "claims with no supporting data or apparent predictive value are not entertained without strong criticism." It's actually quite a harsh environment, for good reason.