You can remove Alt-PHP binaries from cPanel MultiPHP Manager.
To do so set 'yes' or 'no' for the Alt-PHP versions in config file /opt/alt/alt-php-config/alt-php.cfg and run /opt/alt/alt-php-config/multiphp_reconfigure.py.
This script manages SCL prefixes for the Alt-PHP - removes or creates prefixes in /etc/scl/prefixes.
/opt/alt/alt-php-config/alt-php.cfg
[MultiPHP Manager]
alt-php44 = no
alt-php51 = no
alt-php52 = no
alt-php53 = no
alt-php54 = no
alt-php55 = yes
alt-php56 = yes
alt-php70 = yes
alt-php71 = yes
alt-php72 = yes
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