What constitutes a "bad man" in the Roman Late Republic? How are "bad deeds" categorized, and why would military success belong in that category for any Roman in any time period, much less the Late Republic? Why would a Roman general in any time period, from 700 BCE to 400 CE, write a "mea culpa" about his battlefield successes? The Gallic Wars were not villainous soldiers massacring unarmed civilians: they were battles, on battlefields or at sieges or on the sea, between armed combatants. The Romans just won them, usually, due to a combination of superior weaponry, training, logistical organization, and leadership. The Romans did not perceive of the Gauls as hapless civilian peasants, and for good reason: the Gauls were second only to the Germans beyond the Rhine as the great bogeymen of Roman nightmares, the perennial threat from the north which had burned Rome once before and had defeated the Romans on the field countless times since then.
Caesar went to Gaul as governor with the same mandate as all Roman proconsuls: protect the borders of the province, maintain order, extract taxes and resources, and ensure that the dignitas of the Senate and Roman People is not harmed. Upon his arrival, he found a marauding band of Helvetii, about half a million of them, fully intent on crossing through the Roman province on their way to the promised land. Caesar denied their request (see the mandates above). They tried to cross anyway, by force, and were repelled by the quick and prudent measures Caesar took. They then tried to move through the lands of the Sequanni and the Aedui, via the Iura, to bypass Caesar and his province. Many argue that this now had nothing to do with the Romans. This is incorrect. Both the Sequanni and the Aedui, neighbors of the Roman province, had agreements with the Romans, pacts of protection. The Aedui in particular were very close allies of the SPQR, and should Rome not answer their call for protection from an aggressor, the dignitas of the SPQR would be directly harmed. The Helvetii attack on theses tribes also gave Caesar the "legal" mandate to depart the confines of his province and render aid to Rome's allies, as he was the closest and most logical choice for their defense. The senate could have recalled Caesar at any time and sent an alternate force to honor Rome's obligations in Further Gaul. They did not do so. The Helvetii had made themselves a regional problem that needed to be solved, and Caesar found himself in the driver's seat. He did not manufacture it (or if he did, we have no idea how he convinced an entire Gallic tribe to try such a crazy scheme), even though he probably did not complain very much. He got what he wanted, despite the Senate's attempts to park him in a quiet, safe province where he could cause no trouble. Contrary to popular belief, Roman governors did not just rampage all over the Mediterranean at their whim: they were under orders, and their actions were subject to audit upon their return to Rome at the end of their tenure (so see Cicero's Against Verres). Caesar's authority to bring the legions at Aquileia north against the Helvetii stemmed directly from the Senate and the People, as did his authority to recruit further forces. None of that was improper in any way according to Roman custom.
Caesar's consequent destruction of the Helvetii was nothing special for the Romans. Did his legions fall upon a relatively defenseless group of them as they struggled to cross the river? Yes. Were they massacred? Yes. Was it a "fair fight?" No. Would any Roman find this distasteful? No. The Helvetii attack on the Province, and then on Rome's allies, made them hostes, enemies, and Romans killed enemies. Caesar, in fact, seems positively giddy, even via his laconic prose:
Ubi per exploratores Caesar certior factus est tres iam partes copiarum Helvetios id flumen traduxisse, quartam vero partem citra flumen Ararim reliquam esse, de tertia vigilia cum legionibus tribus e castris profectus ad eam partem pervenit quae nondum flumen transierat. Eos impeditos et inopinantes adgressus magnam partem eorum concidit ("When Caesar was reassured via scouts that three portions of their forces had crossed the river, and that a fourth portion indeed was left behind on the near side of the river, at about 3am, having set out with three legions from the camp, he "arrived at" that portion of them which had not yet crossed. He killed a great part of them, having come upon them overburdened and helpless.")
By sheer chance (or by the plan of the gods, he concedes), he goes on to explain that this particular group of Helvetii were the same ones which had inflicted a humiliating defeat on the Romans in the previous generation. Caesar relishes the revenge of it. (Caes. BG 1.12).
From this first year and first conflict with the Helvetii followed the next eight years, each domino falling after the next, as more Gallic tribes become involved on their own initiative or were dragged in. Much of the "justification" stems from the maintenance of Roman dignitas--as each new tribe takes actions which make them hostile to Caesar and therefore Rome, the conflict widens. This is why Caesar tells us he went to Britain: because they kept sending soldiers to help out their cousins in Gaul. Some of Caesar's reasons were more tenuous than others, and the senate could have attempted to recall Caesar's ever-bloating conflict at any time. Caesar was probably overstepping his bounds as governor, though not in a strictly technical sense, but he was certainly not the originator of over-stepping bounds. His colleague Pompey practically wrote the book on overstepping bounds as a provincial governor.
Not even Cicero found Caesar's actions in Gaul distasteful, and the gentle orator and philosopher would have loved to have had some conquest himself in his small, backwater province of Cilicia. He was surely looking to Caesar and Pompey as examples and he was very definitely jealous. Cicero's very minor military skirmishes in Cilicia were not really enough to to earn him a military triumphal parade and attendant accolades upon his return to Rome, but he tried to leverage what little he did have anyway, and in fact was obsessed with the "matter of his triumph," constantly badgering his friends and senatorial allies about its furthering even as Caesar's legions loomed over northern Italia. See his personal letters from late 50 and January of 49 BCE, in which he frequently mentions his hoped-for triumph.
No, no one found it distasteful. Many often mention Cato and his complaining about Caesar, but that had more to do with jealousy and/or political rivalry than any concern for the plight of poor little Gaul. Caesar's commentarii were written for the senate, to be circulated among them, to keep Caesar's name and exploits fresh on their minds (the ancient genre of the commentarii was meant to be battlefield reports, to keep the Senate abreast of developments in far-flung campaigns).