Personally I am mroe sympathetic with the Shapers than the Rebels. If there is anything that the rebellion difinatively shows over the course of the series, it is that uncontrolled shapingis a bad, bad thing. For allof their tyrannical ways, the Shapers realize this and devote a large amount of time and resources towards stamping this out. For example-one of the primary duties of the agents is to hunt down and kill rogue creations before they can do any damage-that doesn't sound very irresponsible to me, and the shaper that created the giant rats you see over the series is stated to have been executed for their actions. This sort of behavior is in stark contrast to how the rebels handle themselves, and irresponsible shaping seems to be one of their most defining characteristics. they create spawners and creators for the exclusive purpose of creating rogue creations, they use cannsiters and geneforges to gain shaping power without any form of discipline that the route of study and experimentation that shapers use provides while simultaneously stripping away the humanity and sanity from its users-a practice that is not only encouraged, but at least in some places *forced* (look at the geneforge 4 intro for evidence) They downplay the risks to recruits (look at geneforge 4 again) and actively look down on anyone who does not use cannisters. While the shapers may have handled the serviles irresponsibly, the rebels in turn created the spawners, creators, unbound and shredbugs with the express purpose of using them irresponsibly. Similarly, their attitude towards gazers would best be termed as 'hands off' despite the fact that these pleasent fellows go around mindcontrolling humans and creations willy-nilly, subjecting them to even worse servitude than what all but the strictist shapers woudl propose.
And however evil the Shapers may be, lets not forget that the rebels demonstrate with ready abandon across the series a desire and capacity to repeatedly commit crimes of equal or even worse stature. Look at the endings to Geneforge 3 and Geneforge 4 and Geneforge 5 to see how the rebels treat civilians, and their desire to exterminate the shapers is even more total than the shapers desire to exterminate the rebels. Compare Alwan's ending in G5 to the Drakon ending or Rawal's ending, for example. They rarely take prisoners and readily torture the ones they do get, invariably to death (where the shapers will sometimes torture, but seem to prefer a quick and tidy execution) Rebels feed prisoners to creations, starve them to death, torture them to death, leave them to die of exposure. Moderate shapers are killed alongside strict shapers overwhelmingly-they rarely compromise. By contrast, the shapers can and do-in Geneforge 4 and 5. Even in Geneforge 5, the 'traditionalist' shaper victory ending is suprisingly light on the rebels, and the player can be rewarded for their loyalty despite being cannister/geneforge warped and potentially a servile. Meanwhile, rebel endings invariably end with massacres and genocide.
In short, as bad as the shapers are, the rebels do everything evil the shapers do and do it to an even more reprehensible degree.