padawanlost:

Nothing
good. The Clones were property, not citizen so a fair trial would be out of the
question. I seriously doubt a government that refuses to acknowledge a clone’s
humanity and citizenship would ever consider to offer him justice. The Republic
was also drowning in debt, there was no money (or interest) to care for the
clones wellbeing, let alone create a whole new system to provide justice for being
who were designed to be obedient and docile.

“There’ll be injuries that a man can survive, but that means he’ll never
be fit for service again. I can’t seriously believe something like that hasn’t
happened in more than a year of this war. And
yet there are no homes for these men, who must surely exist, and we know they
don’t end up being cared for by family—because they have none. So where do they
go?” Besany didn’t even want to think about it, but she had to. The only
answer she could think of right then was that the most badly injured who might
otherwise have been saved were left to die. But some mobile surgical units had
Jedi advisers. No Jedi would let such a thing happen … would they? [Republic Commando:
True Colors by Karen Traviss]

“We have no agreement for
long-term care with the Grand Army. In fact, as far as the Republic is
concerned this patient doesn’t exist, and as he’s been declared brain-dead
by the duty neurosurgical team, we would
normally terminate life support, except he’s still breathing, which is
highly abnormal.” The droid paused as if to check if Besany was following its
train of logic with her inadequate organic brain. “Withdrawal of life support
in his case means withdrawal of hydration or feeding, or both.”

“Starving him to death, for us lay-beings.”

“Indeed. This is clearly
ethically undesirable, so euthanasia will be administered.”

Besany thought she’d misheard, but she hadn’t. “No,” she said, hearing
her voice as if she were standing outside herself. “No, it will not be
administered. I’ll get his care authorized. In fact, I’ll get him moved to
private care.”Did I hear that right? Do
they really put patients down like that? Like sick pets?” [Republic
Commando: True Colors by Karen Traviss]

The clones had no
citizenship, no health care, no pensions and no rights. They were property and every
time a property malfunctioned they called tech support (in this case Kamino).
In case of military punishment – that is not result of malfunction, such as Tup/Fives
case – I believe they would be send to the GAR’s command and they would deal
with them. The problem, of course, was that the GAR command was filled with
guys that did not care for clones rights. If they were okay with sentencing a
16 years old Jedi to death, I doubt they would be too lenient on a clone.

At best, he would end up in
prison and, at worst, dead. I’m not a military expert but I’d assume that
killing your general is frowned upon under any circumstance. Honestly, things
wouldn’t go well for Dogma not because he killed a Jedi General but because he
was a clone. If a Jedi had killed Krell, I doubt said Jedi would end up in
handcuffs (just saying).  

Things wouldn’t go well for
Dogma because he wasn’t a citizen who killed another citizen who had turned on
the Republic. He was a tool that killed his wielder. As Filoni said, Dogma’s
actions were wrong and punishable by the Republic.

[Rex] can’t condone [Dogma]’s
actions through the court system – Basically, Rex can’t legally support it
openly. Personally, he probably might
agree with the situation. He can’t fault Dogma for what happened, but he can
fault him because by the book… Dogma’s
off the book. That’s why Dogma gets arrested. – Filoni

If Dogma is off the book
and his actions were still so wrong Rex could not publicly side with him then
it would be safe to assume Dogma did not have happy ending.