[quote=@Eschatologist]
Seeing as Tyrannus had loads of sith understudies, there is apparently a new sith order, and this war has escalated further and further [likely to draw jedi defectors now that the tide has turned], could I posit that the GAR have implemented anti-sith troops? I ask because it seems common sense to have a squad of anti-sith/anti-jedi troops attached to brigades that are likely to encounter force users.

A squad/squads of snipers, armored flamethrower troops, carbonite throwers, grenadiers, stun-net troops and other nasty anti-personnel warfare specialists who are trained to project emotion and hide their minds from force users would be a relative small cost to protect potentially whole units from single sith.
[/quote]

@McMolly has a great plan to bring the sith back into the fold of things, to which i won't comment much further.  

But yes, you could.  But not as Anti-Sith forces, as Anti-Dark Jedi forces.  Even though the Sith threat still lingers, the threat of Dark jedi would be a much bigger threat imo.  I imagine that once the Jedi forces got wind of Order 66, many felt their relationship with the republic was tainted.  Even though the Jedi Order itself would stand with the GAR, there would be plenty of others that would leave the fold.

[quote=@Exodus]
Would it be acceptable for my character to have been a padawan under Mace Windu?
[/quote]

Could have been and can still be.  He is still alive after all.