Only in as much as the Estonian units fought on the side of Germans. There is a reason most jews who didn't flee when the Germans advanced were killed, the level of collaboration between locals and Einsatzgruppe A was very high..
If you weren't a Jew, you were - in general - treated OK by occupying German soldiers, and least according to accounts I've heard from people who where actually there. The Germans were professional and courteous, the Russians uncontrolled and ravaging thugs.
Funny how Russians always see themselves as 'liberators', not 'occupiers' of Estonia. If this was the case, once they'd driven out the Germans, why didn't they then leave?