Circuit Testing, Verification & Certification Standards for Biomedical Devices
There is nothing wrong in using open source software or hardware to design medical devices. But at end of the day provider of these equipment has to comply with regulation in jurisdiction the devices are sold. I have experiences ubuntu (Linux) computers used in US doctors offices. 

In general in USA and Europe the devices have to be compliant to government regulations such as FDA - 21 CFR 820 (I have attach references below). IEC 6061 which you have referenced is commonly used in both and USA and Europe. This document contains product performance in with respect to EMC/EMI and others. 

One of the major issue with open source software and hardware is compliance to quality requirements. There are many more ...

All in all there are companies starting medical device development work using open source tools but migrate into traditionally accept development process as the product is getting closer to regulatory approval.



References:


21 CFR Chapter I, Subchapter H - MEDICAL DEVICES
Medical Devices; Current Good Manufacturing Practice (CGMP)
Health Insurance Portability and Accountability Act
Premarket Notification 510(k)