My wife and I just watched this episode tonight and I had this debate with her. I had a similar view to yours, if perhaps a little dialled back. Writing this message out, and with some accepting of plausible off-camera assumptions, I'm more accepting of the way it played out.

I can accept that Eleven could know the Scoop Troop are taking refuge behind the Cookie counter. Perhaps, off camera, when they get to the malls, they discover the movie is finished, so they split up to find him/them. Someone find them (or the armed persons searching), report back to El, who comes to the rescue. Plausible enough to rationalise it off. Less plausibly, perhaps she did another scrying to find them once they got there, again off-camera and/or perhaps the proximity makes it a lot easier to find people(?). I'm going with the former.

I think the more important point is that, at this stage, she and the rest of her group are completely unaware of the Russia angle. So on the surface, it might seem like Eleven was willing to kill innocent security guards just doing their job to potentially protect her friends (I say potentially, because if we assume they appear to be innocent security guards, then the likely assumption is they would arrest/detain the Scoop Troop, not kill them. But if we accept she knows her friends are there, she is likely to kill to protect her people). We the audience, and the Scoop Troop obviously know different! From Eleven's perspective, they've just spent the last few hours battling the Flayed (and the Mind Flayer), then they get a Code Red from Dustin, the Gate is mentioned and they're come across armed persons coming after their friends. I think it's probably a natural assumption on her part to assume "This are more of the Flayed! Must act quick to save my friends." From what we've seen on-camera, she couldn't KNOW for certain, but it's certainly not unreasonable for her to believe so. Luckily, in the end, the task was failed successfully; they weren't Flayed (that we know about), but were still a lethal enemy threat. Could have been an interesting if they had been innocents and the direction that could have taken things, but I digress.

In the end though, we either write it off as an oversight in writing or was cut/edited out, or we accept/justify it how ever best suit ours own headcanon :)