TL;DR: Evil is a matter of perspective, so it's a matter of nuanced opinion.

Firefly takes place on the fringe systems, and is told from the perspective of a fringe crew. From THAT perspective, the actions of the Alliance would indeed seem evil:

• The Alliance annexed the outlying systems, then invaded in force when those systems objected to the annexation.
• The Alliance experimented with unethical & illegal methods of population pacification, drugging (and ultimately killing) the entire population of Miranda.
• The Alliance lured children from their families under false pretenses, then proceeded to commit unethical experiments on them, all in the goal of creating the perfect assassin.
• The Alliance created the Reavers, then left them to prey on the fringe planets.
• Rather than admit its mistakes, The Alliance sought to cover up its atrocities by sending assassins and/or mercenaries to kill anyone involved.

Now, from the perspective of a Core Worlds citizen - one who never gets exposed to the dirtier secrets of The Alliance, this might seem like the ideal government. From the perspective of the Serenity crew, however, this just isn't the case.

TL;DR: From the perspective of the main characters, the Alliance is indeed evil.

Firefly takes place on the fringe systems, and is told from the perspective of a fringe crew. From THAT perspective, the actions of the Alliance would indeed seem evil:

• The Alliance annexed the outlying systems, then invaded in force when those systems objected to the annexation.
• The Alliance experimented with unethical & illegal methods of population pacification, drugging (and ultimately killing) the entire population of Miranda.
• The Alliance lured children from their families under false pretenses, then proceeded to commit unethical experiments on them, all in the goal of creating the perfect assassin.
• The Alliance created the Reavers, then left them to prey on the fringe planets.
• Rather than admit its mistakes, The Alliance sought to cover up its atrocities by sending assassins and/or mercenaries to kill anyone involved.

Now, from the perspective of a Core Worlds citizen - one who never gets exposed to the dirtier secrets of The Alliance, this might seem like the ideal government. From the perspective of the Serenity crew, however, this just isn't the case.