You have to use an old PS3 that's jailbroken running an old firmware or certain players (e.g. Oppo or Sony) with specific chipsets running special firmware to rip SACDs.
Yes, MC (along with every other PC CD ripping program) can only rip the redbook (normal CD/PCM layer) of a hybrid SACD. It's not possible for a PC to read much less rip the SACD layer of a SACD disc. I wouldn't recommend ripping the redbook/CD layer and converting that to DSD. That's just a waste of time and hard drive space, in my opinion. That, and PCM to DSD conversions are a lossy conversion.
If you actually want to convert PCM to DSD, just have JRiver Media Center do it on-the-fly via DSP Studio > Output Format > Output Encoding to a DSD format your DAC supports. That way you don't waste hard drive space converting PCM files to DSD. Do note that doing PCM to DSD conversions (especially multichannel) are very resource intensive tasks, so I'd only do that on a PC that's decently powerful.