No, 5mV is ok with a 46dB phonostage. It will be too loud because your SP9 has 21dB gain in its linestage, not because the phonostage has too much gain.
Say you have the Shiit Mani set to 42dB gain - about right for the 2M Red - and you feed that into a line input on your SP9, you will still be sending the signal through the SP9's linestage with its 21dB gain giving you 63dB in total.
Here's the SP9 mkIII manual:
http://www.audioresearch.com/ContentsFiles/SP9MKIII Manual.pdf
On page six it tells you how to reduce the gain of the linestage by 6dB. Unfortunately, that still gives you 15dB gain. However, as heyraz rightly says, the gain of the CD input is 12dB lower than the other line inputs, so you could use that and the volume control would be a bit more user-friendly.
Still, the SP9 is (was?) a pretty expensive preamp with an onboard phonostage. It seems a shame to abandon the onboard phonostage and use a pretty cheap external phonostage instead. A pair of 20dB attenuators at the power amp's input sockets would be my preferred option.