A recent editorial featured on Nature, the International Weekly Journal of Science, acknowledges the need for scientists to respond to the travel ban and outlines the downside to simply boycotting US-based conferences. From the article:

The clear trade-off, however, is that such a boycott penalizes people from Muslim-majority countries already in the United States, who are now effectively stuck there, and so can attend only domestic meetings…It’s unclear who will hear this message, and any impact will mostly hit people who oppose the ban anyway. Making a statement is all well and good, but a protest movement that harms only its allies shoots itself in the foot. The boycotts could be much more fiscally devastating to meeting organizers — mainly scientific societies that actively oppose the ban — than to the US government or economy. And a sparsely attended conference is not useful to scientists from any country.

Research also shows that, with few exceptions, such boycotts have mixed success. For example, the academic boycott of South Africa during the 1980s, intended to oppose apartheid, does not seem to have hurt South African businesses or government at all. Instead, it created rifts between South African academics and those in the rest of the world (S. H. Teoh et al. J. Bus. 72, 35–89; 1999).

The entire article can be found here:
“Academics must protest against Trump’s travel ban — but they should do so productively”