I read the article and understand his concerns. They are valid
concerns. It's not the message, it's the approach.
Think about it:
What kind of responses did he get?
Articles and people saying he's advocating scientists to become
militant atheists.
Of course he wasn't exactly saying that. But if that's the
message that's being received, then he's just preaching to the
converted.
Among the converted, SOME will read him correctly as you did.
Some will not. Among those who bristle against the term
"militant atheist" - whether or not it's used in sarcasm; some
will read him correctly as you did. Some will not.
Sarcasm is poor communication. It will be and has been
misinterpreted.