There would be arguments about this for certain, since many people are still willing to believe that the Avengers and many other heroes could take down the X-Men, whichever team was being represented, without that much trouble. The X-Men have been underestimated more times than a person can easily count, and usually for absolutely ridiculous reasons. But when thinking about what would happen if they entered into a civil war between their own people, especially one in which any intruders would be dealt with swiftly and without any needless posturing, it feels certain that the X-Men, and many mutants that have dealt with them, might rip a significant portion of the world apart since like it or not, if many mutants were going full-out and use their powers without restraint, they could tear the entire world a new one and leave a lot of earth’s heroes and villains reeling. The reason for this is that while the Avengers and many other groups and individuals have their own individual abilities and skills, the X-Men are all naturally gifted, and on top of that, they can cover everything from the physical to the mental to the mystical.
The mutants of the Marvel universe are typically so extremely overpowered that they have to learn how to harness their powers and dampen their abilities so that they’re not walking liabilities everywhere they go. Mutants such as Charles Xavier, Jean Grey, Magneto, Iceman, Legion, Storm, and many others can inflict damage from afar that many of earth’s heroes can’t even begin to combat unless they know what’s coming and how to counter it. But think about if the mutants were to unleash this fury on each other for one reason or another, and then think of those that might try to stand in their way, and what kind of trouble they’d be in if they tried.
One thing to think about is that the mutant race is lousy with telepaths, meaning they have a LOT of them that vary in strength and can affect others mentally or physically or both. This would be a huge advantage in a lot of ways since even if other heroes have resistance to such things as telepathy, there’s not a lot that can be done against someone who can move a chunk of earth beneath your feet from a healthy distance. Disregarding plot armor at the moment, since there’s plenty of that to go around, the base power of many of the mutants in the Marvel universe is often seen as great enough take on several different heroes since unless they’re seriously overpowered, many Marvel characters can’t hope to match the X-Men or any other mutant team on even ground. A large part of this is that many mutants in the Marvel universe are usually hardened survivors by the time they reach their adult years since no matter how progressive the Marvel universe has become, mutants have still drawn the short end of the string a lot of times and are seen as too different than many other heroes, meaning they’re still seen as outcasts that don’t appear to have earned the same regard as other heroes that do the same job and yet get most of the praise.
Granted, the attitude toward superheroes has changed a lot in the last few decades, but the truth is still that some individuals and teams, and in this case an entire, similar species, have been ostracized in such a way that surviving puberty isn’t even enough, they have to fight just about every day of their lives, or find a way to hide and make it appear that they’re the same as everyone else. Mutant acceptance in the comics has never been a huge goal since more often than not they have to continually prove themselves, or they have to work at saving humanity even though humans hate them. But when the frustration and pain that they tend to feel now and again were turned inward at their own kind, it’s fair to think that an all-out civil war between every mutant on the plane would be a huge problem since one has to remember that there are a few of them that are rightfully listed as planetary threats.
When all is said and done one has to admit that plot armor and the person writing the story would be the ones to determine whether or not a civil war between mutantkind would be thwarted or if it would be too much for anyone to stop. But it would be a battle that would be far more destructive than anything the Avengers could cook up, largely because while they have their own powerhouses, the mutants are natural-born powerhouses more often than not, and don’t need to rely on any outside factor to do a serious amount of damage.