Option 1
QUOTE
You may re-roll all of the dice on a single test that did not score a hit.
Option 2
QUOTE
You may negate the effects of one glitch or critical glitch.
No sentence excludes glitches from simply being re-rolled.
The first option is clearly the stronger one, since it is very unlikely that you score a glitch again if you re-role.
But that one option is much stronger than the other, is pretty usual in SR4, so it doesn't prove anything.
Just look for example at the options for called shots (page 161 SR4A):
"Target a vital area in order to increase damage" is way better than
"Target an area not protected by armor". But still there remain some very rare situations where
"Target a vital area in order to increase damage" is actually the better option.
It is similar with this rule. There are some situatios where it is better than re-roling, since it guarantees to remove your glitch. If someone attacks you with 3 hits and you defend with 3 hits and a glitch, and you don't want the glitch, this is the better option.
Another example that I witnessed myself was when I asked my players for an infiltration check. They had set up a diversionary maneuver, so I ruled that only a critical glitch would mess this up. The check was mostly thought to create some tension, because the situation was pretty letal if they would be seen. One unlucky character with the suiting name "Lucky" and a dicepool of 8 rolled a critical glitch. He didn't use the negate glitch option and re-rolled the whole test.
And rolled.......... a critical glitch.
I was pretty baffled.