I see a fairly simple solution. The issue Adobe has is essentially that Ninite is taking away the choice of users to install this software when installing Adobe Flash. Ninite is therefore taking away the revenue that Adobe would get from these installs, if you were to assume that some users actually want them.

Ninite could easily circumvent this by giving people a choice to include the adware. 99.999% of users obviously won't make that choice, but Ninite puts that responsibility back with its users.