Thousands of people rallied in other U.S. cities, most peacefully, and President Barack Obama appealed for calm and understanding, pleading with both protesters and police to show restraint.
I agree that the meaning here is
Most of the people who rallied did so in a peaceful manner.
One might try to read it as
All the people mentioned, thousands of them, rallied in a most peaceful manner.
but that would be at odds with today's reports in the media. Furthermore, the style would be too poetic, or maybe even a bit archaic, for a newspaper report.
On top of that, per comments below, it seems that we can't really read the sentence this way. The part "most peacefully" is not an adverb phrase. An adverb phrase modifying just the verb "rallied" would not have been set off with commas:
Thousands of people rallied in other U.S. cities most peacefully, and...
If it were an adverb phrase set off by commas, it would've modified the whole preceding clause, like this, for example:
Thousands of people rallied in other U.S. cities, most sadly...
Here, most sadly means not "people rallied sadly" but serves as a commentary to the situation as a whole.
Since "most peacefully" cannot be a commentary on the situation as a whole, it is not an adverbial clause, and the sentence cannot be taken to mean "people .. rallied in the most peaceful manner."