I'm not at all a Sam "fan" -- I guess I like Aragorn the best, then Gandalf,
maybe Frodo on holy days. By the way, I think each of these is as well-drawn a
"character" as Sam is. But in response to your provocative post, I don't see
Sam as evil in any meaningful way.
Sam's instincts are for defense. He has every reason to see Gollum as a mortal
threat to his master and to himself. And, frankly, he's right, Gollum is a
killer and a cheat and a liar. So Sam's tendency to contemplate killing Gollum
when the old sneak gets obnoxious is not what I'd call evil. Indeed, it's clear
to me from the context of the quotes you give that Sam would never actually act
on his murderous impulses, or more correctly, fantasies, against Frodo's will.
Sam works for Frodo, and puts up with Gollum because Frodo bids him to. But he
disagrees with his master's decision, and takes thought to how to prevent what
he foresees will be the ultimate murderous betrayal.
What is being acted out for us through Sam's eyes is a struggle between faith
and prudence. Frodo has an unjustifiable faith, based on his education from
Gandalf, that Gollum will somehow serve him: "our fates are bound together."
Sam, coming from a lower level of motivation, cannot see the sense of hiring a
pathologically criminal freak to guide them into the heart of darkness, and
steadies himself by fantasizing about doing unto Gollum as Gollum would do unto
him, only doing it first.
Paul Kocher comments that Aragorn had a similar problem with Gollum, and took a
similarly realistic approach to the problem:
After capturing, subduing and transporting Gollum from the Marshes to Lorien,
"...[Aragorn] never comes close to winning Gollum's loyalty as Frodo does, but
then he never suffers the concomitant betrayal, either. What Aragorn lacks is
the conviction of Gandalf and Frodo that a free Gollum will perform ultimate
good that Gollum himself does not intend. But this is an intuition beyond all
reason." - Paul Kocher, Chap VI, Aragorn, in Master of
Middle-earth, Houghton Mifflin, 1971.
It is Gollum who is evil, or mostly evil. Sam, like Aragorn, is good, but must
deal with the evil in a practical way.
P.S. I don't find the "dark cloud that had fallen on his own heart"
particularly ominous. At that point they are crossing the Dead Marshes toward
Mordor, and the Shadow is growing ever closer. Sam does not have the Ring, but
he is nevertheless affected by the spiritual stress of the environment. One
dark cloud in the heart does not a villain
make.

"Wake up and smell the coffee."
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