But that's the point you are not converting. You are taking suspect data and transferring it. NTFS has metadata attached which malware can and does use if your security has been compromised.
And in this case security most definitely has been compromised.
Samba is not a filesystem it is an application which allows MS clients access to UNIX system resources. Its the well proven UNIX security which does the work not samba. The fact that NTFS was designed by the open VMS chap to incorporate the security of the well proven UNIX method is fact. The fact that Microsoft decided to add features to it which allowed the security to be compromised is also fact.
It is also fact as well that given the option large% of home users will not follow best practise, will not have that 3rd sense in the back of there heads to tell them not to click on "ok". Even if the browser asks them "are you sure you want navigate away from this page" they will click "OK" where as you and I will kill the process.
Its not a fundamental problem with NTFS it is a problem that most computer users don't have a bloody clue what they are doing. Which as admin's we used to lock down, turn off numerous features to protect our systems.