Go to your descr_strat.txt found in C:\Program Files\Activision\Rome - Total War\chivalry\data\world\maps\campaign\barbarian_invasion (I think, not 100% sure what the minor and grand ones exactly are)
In this file at the top should be a list of playable factions then below a list of non-playable ones. Cut and of the muslim factions you'd like to play with into the playable section. Something like this:
Code:
playable
gauls
britons
germans
romans_scipii
romans_senate
carthage
dacia
numidia
spain
scythia
parthia
pontus
armenia
thrace
greek_cities
macedon
egypt
end
unlockable
end
nonplayable
seleucid
romans_brutii
romans_julii
slave