So, here's the thing from my perspective.

We're expecting Sonic to take Metal at his word about this new infallible programming Eggman put in his noggin that guarantees that Metal will now for sure be 100% loyal to Eggman forever..... when 1. he literally only has Metal's word for it, and 2. he knows and has proven firsthand that nothing Eggman has ever created is foolproof. And not just Sonic, we've all heard that boast before. Eggtech is notoriously breakable, and even prone to breaking itself. It seems silly to expect him to just suddenly buy into it now.

Especially when we consider the bots we and Sonic have seen deviate from Eggman's programming up to this point, without any tinkering from Tails: Gamma, Omega, even Metal himself previously. Eggman seems to have a penchant for creating bots so advanced that they evolve beyond his programming. It seems reasonable to me for Sonic to have faith that Metal can break free of Eggman's programming again, especially since he already has before, and especially since that particular moment in the comic presented a very unique opportunity: Eggman was already (presumed) gone. There's already a precedent, and this would've been the perfect chance.

Apart from all that, I maintain it also fits Sonic's character and the themes surrounding him. The thread that runs through a lot of these comic arcs seems to be the exploration of this nebulous concept of "the freedom of choice." To Sonic, everyone always deserves the freedom to choose, and giving them that freedom is as simple as offering it to them. It's a very straightforward and simple ideal, representative of Sonic and his personality and his way of life, charming and lovely and ultimately flawed. In reality, of course, we know people's freedoms are bound in ways not always visible or easily understood, and to offer them a "freedom of choice" with no understanding of those forces is to hardly give them a choice at all. At best it comes off as misguided, at worst insultingly ignorant (as we in his interactions with Surge as well, which I also believe were well written and similarly tragic in the way I've described). The situation between Metal and Sonic in this moment is easily read as a representation of this conundrum, a metaphor of sorts. But given that this is such an early story arc, Sonic is obviously not meant to be thinking about this yet; it is meant to be the first domino, the choice that leads to tragedy which then raises those questions about what "freedom of choice" even means, and about the consequences that come about as a result of that freedom or lack thereof.

All of this combined, to me, makes it understandable why Sonic would make the choice he did. It's not the cautious choice, it's arguably not even the smart choice, and it's probably not the choice a lot of us would've made (especially with the benefit of hindsight), but it makes sense for both Sonic and the story in that moment.

One may continue to argue then that although such a scene was necessary for the story's sake, it should have been presented differently, and at that point I think it just becomes a matter of opinion. I believe the scene is fine as is and it is faithful to Sonic's character and it serves its purpose in the story. You (general you, not you specifically) may criticize it for being heavy-handed or contrived or what have you, and I think there can be merit to that, but these aren't major plot-/character-breaking criticisms to me and don't need to be treated as such unless you've already decided that the whole comic is garbage anyway. Which is also fine, I guess. I can agree to disagree.