Using a rag dampened with mineral spirits will NOT damage the rubber roof nor "dissolve" it unless you are pouring it on. Even then I doubt it would. I was not advocating pouring it on. I've used mineral spirits on my rubber roof and soft plastics without damage. And mild soap and water will not clean the roof enough for Eternabond to work well. In fact, you might be interested to know that Eternabond recommends using acetone because it softens the surface to increase the bond with the tape. I find mineral spirits to be far less caustic.
http://www.eternabond.com/articles.asp?id=169