Rich is correct in his assessment. Placing a current day preamp in front of a vintage integrated is problematic. I would point out that the Freya+ has a signal to noise ratio of around 100 db (very good for a preamp), while the Sansui is around 80 db (meh). The higher SNR, the better. Basically, the Sansui has more background noise which may lend itself to a "warm" sound, but in general, it means that there is more distortion present that results in said described, "warmth". Hence the Freya+ created a cleaner sound that when pushed through the Sansui, you lose "warmth", largely due to the fact that the preamp section in the Sansui was inferior and lent itself towards the Sansui analog sound of it's day, as Rich pointed out. And, as with all older gear, the Sansui may or may not have been re-capped- or it may have been re-capped with parts that were slightly different than what was original- which would lend itself to a different sound.
If you listen with the Freya in passive mode, you will be hearing the amplifier section of the Sansui. That should give you all the information you need on what kind of sound it is contributing. "Muddied" would likely be your adjective when you do that.
I have the Wharfedale Linton's paired with a Rogue RP-1 and an NAD C298. Before I purchased the NAD C298, I used an NAD 275BEE. As for SNR, the difference in those two amps are some 20db's apart. That is distinctly audible. The C298 sounds cleaner, more articulate, and less muddied. I remember comparing the two amps and realized that the 275 provided a better soundstage (a bit more present and wider) but that was because of the distortion. When listening over long periods of time, that soundstage became an aggravation to my ears and it was a relief to pair the RP-1 back up with the 298.
I would suggest finding a stand alone amp with an SNR of 90db or higher to match with your Freya+. You have simply done what everyone else has done, you have upgraded one piece of equipment, which opens itself up to another piece of equipment being the villain. Move on, don't try to make the Sansui better, it is as good as it's going to get stand alone.
You have entered the world of separates. Use equipment that matches well with one another and use quality cabling to connect them together. Your starting point is now your preamp (a good one!), and your streamer and speakers are fine. I love my Linton's, feed them better electronics and they will respond in spades.