I would seriously get a solicitor involved as soon as possible - it sounds like judgement shouldn't have been made - but if it is the name of the company, then the company will be liable.
This needs to be sorted asap as the CCJ is public information - our local paper publishes on a weekly basis companies who have has CCJs registered against them- and you don't want a bad reputation (I assume).
It will also (obviously) affect both the credit rating of the company as well as you as individuals (when applying for credit, most finance companies will do a director search and a basic company search - which will show the CCJ)