Depending on how you wargame that out, it depends on a lot of things that have never been made explicit in the canon verse.
How long have Muggles (specifically, the U.S. government) known about wizards? How long have they been making plans? How much information do they have about the wizarding world? Do they have any wizards on their side? How effective is Imperius, long-term and against many people? Are Muggles actually completely incapable of devising any means to resist, detect, or counter magic? Even if they have had centuries to study the problem, possibly even with magical allies?
If it came down to all-out genocidal warfare, the sheer number of Muggles with modern weapons would be hard to counter. At the very least, there would be a high body count on both sides.
Muggles vs. Wizards
How long have Muggles (specifically, the U.S. government) known about wizards? How long have they been making plans? How much information do they have about the wizarding world?
Do they have any wizards on their side?
How effective is Imperius, long-term and against many people?
Are Muggles actually completely incapable of devising any means to resist, detect, or counter magic? Even if they have had centuries to study the problem, possibly even with magical allies?
If it came down to all-out genocidal warfare, the sheer number of Muggles with modern weapons would be hard to counter. At the very least, there would be a high body count on both sides.