Quite a few plant viruses replicate within the chloroplasts (Tobacco mosaic virus, tymoviruses, Potato mop top virus, etc.) and some replicate in the mitochondria (Tobacco rattle virus and Cucumber green mottle virus) so yes.
http://www.pnas.org/content/86/12/4496.full.pdf
http://www.frontiersin.org/plant-microbe_interaction/10.3389/fpls.2012.00290/abstract
http://books.google.com/books?id=TvsWPMcW-fsC&pg=PA419&lpg=PA419&dq=plant+viruses+that+replicate+in+chloroplasts&source=bl&ots=UQg7Lz4Fvd&sig=goWG2cI_RbLwDju02tfxQWMwQ5k&hl=en&sa=X&ei=-Iu9Uum7LYb1oATm8oG4Bg&ved=0CGkQ6AEwCA
http://vir.sgmjournals.org/content/91/8/2102.abstract
It is very common to find that viral proteins interact with mitochondria in order to control apoptosis. A good review is "Viral proteins targeting mitochondria: controlling cell death" by Patricia Boya et al (not my paper, by the way). BBA-Bioenergetics 2004, Vol 1659(2-3) pages 178-189. That paper is getting a bit old, but it is a great place to start.
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