Yes, the reader is meant to think that Connie is murdered at the end, for two reasons. First, because Oates said she based the story on a series of murders of young girls in Arizona during the 1960s. Second, the last sentence gives us the impression that Connie is headed to her grave: "'My sweet little blue-eyed girl,' he said in a half-sung sigh that had nothing to do with her brown eyes but was taken up just the same by the vast sunlit reaches of the land behind him and on all sides of him--so much land that Connie had never seen before and did not recognize except to know that she was going to it."
The ending is open to interpretation. What we do know is that she has decided to save her family and go away with Arnold. There is a sexually-threatening innuendo to the scene. She seems to go dead inside at the thought of it. Whether or not she dies, we do not know. Arnold states that he thinks she will grow to accept it, so he has no immediate plans to kill her.
That is the beauty of the story. Oates never tells us, but the ominous foreshadowing given throughout the story suggests that things may have not ended well for Connie.
No one really knows what really happens in my English class we think that she was either killed or raped or both. Still the ending is in question. if you really want to know you can write up your own endind to it.