MalikX
Superstar
The only thing I can think of is that Rhaegar was in line to be king, and kings can legitimize whoever they want. So at best, his plan was to have Jon as a trueborn son and legitimize his other children from the dissolved marriage as well. But even then, I could see that being the prelude to a future civil war where certain factions believe Jon should be first in line to inherit the throne and others believe Aegon should be.
It definitely could have led to that...that's how the Blackfyre Rebellion/Dance of the Dragons started. Rhaegar was on his Bran shyt. As long as the PTWP was born, he aint care about the collateral damage.