"We can come up by ourselves."
可以 can be used for permission or alternate possibilities.
The way I understand the Chinese, it could mean:
We can (have permission to) come up on our own.
(Might say this to a doorman, receptionist, or security)
We can (are able to) come up on our own.
(The listener doesn't need to come down and show them the way up)
That's my take, but it would be nice to hear from a native speaker.