How can I protect my SMPS feedback voltage divider from loading effects?
Use higher value resistor values in your divider, to give better power efficiency, and hopefully have less effect on other systems/loading. Don't set your feedback resistance too high though, stay below 1M Ohms. 

The probe or pins of a multimeter WILL affect the feedback resistance in parallel with ground, and therefore adjust the output voltage during operation. The best way to see the feedback voltage is to use a very high impedance probe set, which may still affect it a little bit, but much less than standard probe sets. 

Further reading on resister dividers and their use in DC-DC converter feedback signals, check this Texas Instruments Application Note