Shooting is the best way to use skinks. I would only charge if you think you can get a rear charge on a unit to help out your saurus with a +2 CR.
Fleeing or holding is definitely an choice with many factors you need to consider. Is there a more valuable unit behind your skirmishers? Will tying up the charging unit for a turn of combat allow you to get a flank charge on the unit? Will fleeing pull that unit out of position? Do you think you can kill enough models with stand and shoot to panic them? Etc, etc. I'll gladly throw a unit of skinks under the bus if it means stopping a flank charge on another unit.
Javelins and shields vs blowpipes. Both have the good points and bad points. I actually busted out my statistics book a few weeks ago pondering this question. Here are some stats that I've come up with:
Assume we are attacking a typical unit (T3, AS4+) with a unit of 10 skirmishers.
BLOWPIPES:
Short range, single shot: 5 hits, 3.3 wounds including 1.6 poisoned, 1.6 unsaved wounds.
Short range, double shot: 6.6 hits, 5.0 wounds including 3.3 poisoned, 2.5 unsaved wounds.
Long range, single shot: 3.3 hits, 2.5 wounds including 1.6 poisoned, 1.2 unsaved wounds.
Long range, double shot: 3.3 hits, 3.3 wounds including 3.3 poisoned, 1.6 unsaved wounds.
Move, Short range, double shot: 3.3 hits, 3.3 wounds including 3.3 poisoned, 1.6 unsaved wounds.
Move, Long range, double shot: 1.6 hits, 0.8 wounds including 0 poisoned, 0.4 unsaved wounds.
JAVELINS
Short range: 5.0 hits, 3.3 wounds including 1.6 poisoned, 1.6 unsaved wounds.
Long Range: 3.3 hits, 2.5 wounds including 1.6 poisoned, 1.2 unsaved wounds.
Pretty much the same statistical killing power and Javelins will never require a 7+ to hit, under normal circumstances. Additionally, javelins allow to stand and shoot no matter what, and you get a 6+ ward save in close combat. But then again your unit costs a little bit more.