You can remove aggregates by ultracentrifugation, gel filtration chromatography, or filtration through a 0.1 µm filter.

The size analysis itself should not cause any aggregation. There is no prior treatment required, however purified and filtered samples may give an answer closer to your expectation (because even small amounts of aggregation/dust/air bubbles can skew the result). For pore size, even as low as 20nm might be possible. Or centrifugation may be preferable to minimize potential sample loss.

For electrophoretic mobility / zeta potential analysis, proteins are best measured with the diffusion barrier method to keep them away from electrodes.

http://www.materials-talks.com/blog/2015/11/24/diffusion-barrier-method-the-practical-details/

http://www.materials-talks.com/blog/2016/01/21/zetasizer-sensitivity-for-protein-dls/