If only to play the devil's advocate, Thieves Cant is just a name for a secret language. Change the name, change the feature. Call it Doublespeak, Ranger Tongue, Drow Sign Language, Insinuation or any other hidden or subtle language and nothing in the function of the ability changes except who is using it. If you want to call this a houserule, you'd be within your rights to do so, but I've yet to encounter a GM that didn't alow it at their table.
"Thieves Tools" are also misnamed IMO. There are any number of legitimate professions that have need of tools for picking locks or disarming traps. Law enforcement, entertainers (specifically escape artists) and anyone involved in home defence (e.g. locksmiths), let alone those who learn it out of interest or as a hobby, might have use for such equipment. Just because a thief might use a hammer to break a lock does not mean that every carpenter or blacksmith should be tarred with the same brush.
Again, what makes this any less "honourable" than e.g. Precision Strike, another clearly valid interpetation of what Sneak Attack actually is, as opposed to the overtone of what it's called in the book? The actual function of the feature is to give its user additional damage whenever they have an advantage in combat. Yes, "sneaking" is one way to do this and that carries certain negative connotations, but is far from the only one. You might also call it Master Stroke, Combat Flourish or any number of non-criminal or non-murderous names and be equally applicable.Their primary ability however is sneak attack. This ability, is as the name suggests, something whose greatest utility is when attacking someone unawares. This is definitely dishonourable according to any basic definition of honour (at least the common ones) and is at its core an 'assassin-like' ability. Another word with very evil overtones.
If we apply the same standard to the Fighter as you have the Rogue, then even Extra Attack has overtly aggressive overtones. How about the Barbarian and their Rage? Yet both of those classes have been universally pegged in the Neutral category, let alone the Paladin and their Smites (both feature and spell). Compare this to other features of the Rogue such as Uncanny Dodge or Evasion, which are explicitly defensive in nature. In many respects, the Rogue can be seen as a defensive, less aggressive Class that has a single feature that allows it to exploit weakness in combat. For the vast majority of the Rogues features and their actual function, they are a survivor, not an aggressor.If we compare it to fighter. Well, who are fighters? It is very easy to be a soldier, or a guard or some other security-based (and defensively-based) martial character. While war is a complex topic, in general, it is easy to reconcile being a soldier, guard or similar profession without leaning into the cut-throat mercenary type. So fighter are at least more neutral and generally skew 'good-ish'.
Ask what the Rogue is good at; running away (Cunning Action), evading damage (Uncanny Dodge, Evasion) or control (Slippery Mind) and being good at their selected fields (Expertise, Reliable Talent). Are any of those features explicitly "evil" or even have a negative connotation? The fact that Sneak Attack is prominent on the Class table goes a long way towards misinforming the reader as to what the Rogue is or is capable of; the reality is that Sneak Attack is, perhaps, the least of the Rogues (non-ribbon) class features, serving only to keep pace in the DPR game compared to those better suited to it.
In short, Rogues have a bad rep because their PR isn't very good...or perhaps because they like it that way