There were several application protocols in use at the time of the TCP cutover (1981?), including ftp and telnet. We didn't just throw them away, we ported them over from TCP's predecessor NCP. The one we did throw away was email, which was not a separate protocol, but was implemented as part of ftp. We got rid of that and replaced it with smtp. But the new ftp/tcp servers still supported email for several years as a transition.
It turns out that FTP has gone through some stages of specifications, dating back to 1971. TCP originated in 1974, according to Wikipedia that is.
The current version of TCP (RFC 793, 1981) predates the current version of FTP (RFC 959, 1985), and normality is restored.