Hi,
Did you properly configure your Analytics - normally someone who goes from the main site to the subdomain should not be measured as a bounced visit. If you are using Google Analytics, you can find here how you should change your trackingcode (if you use the async version) - here if you use Universal Analytics.
As google is not using your analytics tool to determine the bounce rate but uses it's own sources, this will have no impact on your rankings.
Apart from this issue, in general it is better to have everything on the main domain. You could check this presentation of Rand on this topic. You should check with your technical people if it wouldn't be possible to move the Magento to a directory of the main domain.
Plenty of sites are using different technology on different parts of the server, without it being visible to the visitors. As long as the user experience is not affected this should not be a problem - so there is no reason to put everything on one technical platform.
rgds,
Dirk