From Wikipedia:
征伐(せいばつ、conquest または subjugation)とは、反乱を起こした勢力を鎮圧したり、反社会的な犯罪集団・賊などを、武力で処罰(懲罰)したりすることをいう。実際にはプロパガンダ(政治宣伝)として、公権力を背景とし、政治的に敵対する勢力に対して武力行使(攻撃・侵攻・侵略)をしかけるときに使われることが多い。対象は敵国や異民族の場合もある。「征服」に比べて「政敵・及び政府の敵を懲らしめる」という意味合いが強い。
So it's not a neutral word but is a subjective and condescending word that does have a connotation of "defeating the evil", "suppressing insurgency" or even "showing power to savage people". In reality, it's often merely a means to justify what a government is doing; it has been used against what they considered as "public enemies". Indeed, 討伐征伐 sounds "glorious" as long as you are on the government's side. On the other hand, modern historians, who need to be objective and understand the meaning of this proverb, tend to avoid 征伐.
討伐 also has a very similar connotation, but it's used with a single (subjectively "evil") enemy or a small group of enemies (e.g., 勇者が魔王を討伐する).