Evil is also not good, like bad, but usually a bit deeper, more mature, and doesn't just steal your last bar of chocolate - it kills your friends, kicks the dog, plots world domination, and then steals your last bar of chocolate.
Things which are cute are frequently evil (cf. bunnies, kittens, praying mantises, Molly Rath), conversely evil is not always cute.
The PPC and OFUs consider Sues and Stus evil. Likewise, Sues and Stus consider the PPC and OFUs evil. If you use relative morality, it mostly depends on your point of view and what side you're on; if you use absolute morality, only one group can be right (though both may be wrong). Some consider the PPC's actions an attempt at mass murder or genocide; others believe they are a necessary evil; and still others believe that killing Sues is a justified part of war. Others believe that any character written badly enough to be a Sue is also too badly written to be sapient, so that killing a Sue is more like killing a rabid animal than like murder.
It should be noted that some Sues and Stus, including canon Sues and most historical Sues, are not direct threats to the canon, and don't do much damage to it. These Sues/Stus are usually recruited or left alone entirely, as evidenced by the prevalence of reformed Sues becoming agents. Notably, some agents (such as Acacia Byrd) also believe the PPC and OFUs are evil. One wonders why such agents fight the Sues if they believe they work for the villains.