If my opponent uses "Mirror Shot" on my Active Pokemon, would I still have to flip a coin for my attack if I retreat?
No, retreating would clear the effect of Mirror Shot.
Source: Undaunted FAQ (2010-09-09), PUI Rules Team (2010-09-09)

Relevant cards

Note: All applicable cards may not be listed below.
COL1_5
DPP_DP32
DPP_DP32
HGSS3_3