If i were a unit under your command, i'll probably also rout and desert.
On another note, i haven't had any "big" moral problems in STW2, especially not samourais.
I also believe no army routs after loosing "just a few men". Probably an underestimation from your part.
Lastly, general being "close" doesn't do much, BUT, he has an active skill to actually push your troops to fight. Use it in the right situations.
Loss of moral comes from :
- a lot more ennemies
- units under fire
- units loosing in combat against another unit
- unit being flanked/attacked in the rear
Consider ashigarus have pretty low moral too, so it's normal. There's also an easy tech in the war tree to give +1 moral, might be usefull.