You bring up a valid argument actually. The problem is that, EU membership as you mentioned kicks in before the actual membership also since it makes you follow certain guidelines even before the actual membership.
Hence is the recession situation, which allowed pro-EU countries to recover faster from the collapse. On top of that maintaining gdp growth on the same level as less developed countries is harder when you are more developed which is also an abnormality. (Percentage wise)
A good example of this is America and China. Everybody understand that America will grow slower compared to China because America is already heavily developed. (Percentage wise)
I'm sure there is some truth to this. Yet, there are other factors which could plausibly have contributed to the different experiences of Eastern Europe vs former SU countries. First, the latter were more integrated into the Soviet Union and hence would have been more negatively affected by its disintegration. Second, the Eastern European countries, especially those closer to Central Europe, would have been attractive destinations for investments and outsourcing regardless of EU-membership. This is not only due to geographic proximity, but also long-standing ties and cultural similarities between these countries (the same effect can be observed in former Yugoslavian countries).
And third, if you look at the growth rates starting in 1996, which as mentioned is the first year for which data is available for all countries and at which point pretty much all of them had returned to growth, you can actually see a moderate catch-up by most of the former SU-countries. But even if you discount this, your argument about maintaining GDP growth fails to explain why Bulgaria and Romania are still lagging behind and why, for instance say, Ireland, despite its troubles during the eurozone crisis, has managed the most stunning catch-up of all EU-countries. In fact, if you include Ireland in my above IMF chart, it outstrips all Eastern European EU-members in terms of average GDP growth despite being more developed during the whole period.
Hence, I would argue that, while it's certainly possible that EU-membership had a positive effect of GDP growth since the fall of the iron curtain, we need to take these other factors into account, at least as a possibility.