Aside from polymorphing the target, the best you can do is a straight roll.
From the rules for advantage and disadvantage:
If circumstances cause a roll to have both advantage and disadvantage, you are considered to have neither of them, and you roll one d20. This is true even if multiple circumstances impose disadvantage and only one grants advantage or vice versa. In such a situation, you have neither advantage nor disadvantage.
If they have advantage from spell resistance, and you can somehow impose disadvantage, then the result is that they roll a single d20 for the saving throw.
I asked a similar question, if there was any way to give true disadvantage to creatures with spell resistance: Is there any way to give proper disadvantage on saving throws against spell effects to a creature with Magic Resistance? The only solution was polymorphing the target into something without spell resistance, and this isn't a great solution. In their answer to my question, Szega writes:
You might have a bit of trouble targeting them with other effects as they are now a beast and not what they were before, but effects that could affect both will persist even when polymorph wears off.
You also cannot damage them properly, but in exchange they are helpless as well.