Yes, you can replace the engines with a shipyard refit, but it will almost certainly cost more than building a new (Ion-engined) cruiser from scratch. So while not technically true, it will probably feel like you are stuck with slow pieces of scrap.
To do it, go to the F5 'Class Design' screen, use the 'Copy Design' button on your nuclear-engined missile cruiser design, then 'Rename Class' to Mark II, or -B, or whatever, swap the engines, lock the design, go to the F2 'Population & Production' screen, 'Shipyards' tab, select the cruiser shipyard, choose 'Retool for Selected Class', choose your Missile Cruiser Mark II, hit 'Set Activity', wait ~6 months for the retooling to be done, move an existing cruiser to the colony with the shipyard on it, choose the shipyard, choose refit, choose your cruiser, choose your Mark II cruiser design and assign the task to a slipway.