While I see no problem in good relations with Russia, we're treading on really difficult grounds there. NATO and the relations to the US shouldn't be ignored too much (they're in a sorry state since Schröder imo), and maybe even more importantly, we have to be considerate of Poland. They're Germany's most important neighbor country after France and will only become more important in the future with their economic growth. And I can understand that any German-Russian cooperation gets them into alert condition.
I don't think it's that difficult ground to tread. Russia would want co-operation with Germany, and Germany would want co-operation with Russia. Germany has that co-operative spirit backed up by the EU, so Poland should not really get all that concerned over it. It's not like good relations with one precludes it with the other, even if they aren't besties.