When you use metal cutting blade with more teeth, they the will cut aluminum much better.
Can aluminum channel handle the heat depends on the ratio of how much metal to LED power and how good you contact of the led to the heat sink is. Assuming you have good contact point your heat sink should not go over 50 degree C after 2 hours of operation. Consider add a fan.
Decent quality rotary saws for wood will do a fine job in aluminum as well as aluminum is generally pretty soft. For example a mitre saw equipped with a good quality carbide tipped blade (of higher tooth count) will work great in cutting extruded aluminum. Of course the usual reciprocting saws like jig-saws etc. will also work well with a coarser blade for metal (don't use very fine metal blades as they may plug up with aluminum chips). Same goes for a hack-saw.