I've re-read it and still kindly and respectfully disagree about the meaning of that excerpt in isolation. Whatever the implications of this interpretation are, I have no idea because I'm not familiar with the work (however naïvely).
Here's a detailed breakdown of my take:
I do not imply, for instance, that we should always suppress the utterance of intolerant philosophies;
The key word here is always, so, intolerant philosophies shouldn't always be suppressed.
as long as we can counter them by rational argument and keep them in check by public opinion, suppression would certainly be most unwise.
The condition for not suppressing intolerant philosophies is if they can be kept in check and countered by public opinion and rational argument.
But we should claim the right to suppress them if necessary even by force;
Reserve the right to suppression if necessary..
for it may easily turn out that
Because the following things might easily happen:
they [the intolerant] are not prepared to meet us on the level of rational argument, but begin by denouncing all argument they may forbid their followers to listen to rational argument, because it is deceptive, and teach them to answer arguments by the use of their fists or pistols.
An example of what may occur when the first approach fails due to essentially bad faith, and the reasoning for why to reserve the right to suppression. But it doesn't frame violence as the threshold for when to apply that suppression.
Anyway, that's my take. I'm still assuming this quote is accurate - I haven't checked it.
And once again I'm absolutely not agreeing with these positions or assertions about the suppression of intolerance, this is just how I understand the text.