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Their second site, hosted elsewhere, has plenty of good content and links, and just needs a bit of optimising.
They want Domain A pointed/redirected to Domain B, (their company was bought out so changed name), but in view of the problem with the virus having just been removed from Site A, is it a bad idea to redirect it to Site B, from an SEO perspective?
If so, how long should we wait before implementing the redirection?
If not, site A is basically just in a waiting period before it gets hacked again, so you'd be putting site B at unnecessary risk by sending its visitors to site A.
In addition, anyone who visited site A during the time it had the virus will probably avoid the site from now on. Getting a virus alert is a strong negative experience, and getting a virus is even worse, so there are probably people that site A has lost forever.
So site A's security practices are questionable, it has a recent history of being a dangerous site, and its brand is tarnished. From the standpoint of human behavior, I see those as problems.
From the standpoint of SEO, the recent problems might not affect how search engines rank the sites, providing they're no longer flagged as dangerous in any databases and they stay clean. If site A was flagged as dangerous by Google, the fact that the incident happened will be reported on its "Safe Browsing Diagnostic" page for at least 90 days.
Just my perspectives.