We need to suspend your site immediately on notification of Malware being present, because of the security threat it presents to the server, other hosting accounts etc. The malicious software may be being used to generate SPAM or SCAM mails, Probing other sites on the internet etc.
As a end user, if Google scans your website for Malware , it will blacklist your site or flash a warning to enduser’s stating this site may harm you. Google ranking and your sites popularity will go down. Hence it is important to fix the contents on priority.