He was basically a hired hand for the Separatists, so I guess that led him to fight against the Republic and the Clones; technically Jango didn't personally fight against them cause Samuel L. Jackson decapitated him before they arrived on Geonosis.
I also wouldn't say sharing the same DNA with clones is the basis of a deep relationship; in the end, Jango is a bounty hunter and probably felt little to no connection with his 'children', as you say.