I highly doubt the latter. If anything the former seems more likely. I'm even wondering if she has romantic feels for Tomo. But I also get how friends can also get jealous.
It's most likely the first one. It's been mentioned throughout the manga that she's highly possessive over tomo, and that tomo is her precious person. Wether this is romantic or not is questionable, but Tomo is Misuzu no.1 (as implied by carol). She doesn't really have any romantic thoughts about Jun either- she was using him in middle school to bridge a gap and is using tomos want to get closer to Jun as a way to bridge a gap. She just doesn't want to be the third wheel and be left out I think, though i doubt tomo would 'cast her aside'er as soon as jun gets his head out his ass
Oh, she feels something for Jun... like murderous intent, hate etc. LOL
I got two cents for what Misuzu said. It's either:
1. She thinks Tomo will be taken away coz Tomo's her only beloved best friend.
2. She feels something for Jun and she ain't aware of it yet... or not at all.
I hope it's the former. henk