He's really quite cryptic here. But I think this is how Emma might be interpreting it in her mind:

"Yes -- I have called there... She is a woman that one may, that one must laugh at; but that one would not wish to slight. It was better to pay my visit, then" --

Emma's interpretation: "I didn't WANT to call on Miss Bates but civility demanded it. So I felt it was better to pay my visit to her FIRST, then I could be free to devote my remaining time solely to YOU."

"In short," said he, "perhaps, Miss Woodhouse -- I think you can hardly be quite without suspicion -- "

Emma's interpretation: "In short," said he, "perhaps, Miss Woodhouse -- I think you can hardly be quite without suspicion -- that I'm desperately in love with you!"