This does not seem to be the case if you upgrade to mysql55 manually instead of using yum-plugin-replace:

[root@mysql55 ~]# rpm -e --nodeps mysql mysql-server
warning: /var/log/mysqld.log saved as /var/log/mysqld.log.rpmsave
[root@mysql55 ~]# ps axuw | grep -i mysql
root      2016  0.0  0.5  63840  1316 pts/0    S    22:18   0:00
/bin/sh /usr/bin/mysqld_safe --datadir=/var/lib/mysql
--socket=/var/lib/mysql/mysql.sock --log-error=/var/log/mysqld.log
--pid-file=/var/run/mysqld/mysqld.pid --user=mysql
mysql     2066  0.0  9.1 188404 23996 pts/0    Sl   22:18   0:00
/usr/libexec/mysqld --basedir=/usr --datadir=/var/lib/mysql
--user=mysql --pid-file=/var/run/mysqld/mysqld.pid
--skip-external-locking --socket=/var/lib/mysql/mysql.sock
root      2092  0.0  0.3  61188   824 pts/0    S+   22:19   0:00
grep -i mysql
[root@mysql55 ~]#
[root@mysql55 ~]#
[root@mysql55 ~]# yum install mysql55 mysql55-libs mysql55-server
Loaded plugins: replace, rhnplugin, security
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package mysql55.x86_64 0:5.5.9-1.ius.el5 set to be updated
--> Processing Dependency: mysqlclient15 for package: mysql55
---> Package mysql55-libs.x86_64 0:5.5.9-1.ius.el5 set to be updated
---> Package mysql55-server.x86_64 0:5.5.9-1.ius.el5 set to be updated
--> Running transaction check
---> Package mysqlclient15.x86_64 0:5.0.91-1.ius.el5 set to be updated
--> Finished Dependency Resolution

Dependencies Resolved

==================================================================================================================================================
 Package                                Arch
   Version                                  Repository
     Size
==================================================================================================================================================
Installing:
 mysql55                                x86_64
   5.5.9-1.ius.el5                          ius
    7.4 M
 mysql55-libs                           x86_64
   5.5.9-1.ius.el5                          ius
    1.2 M
 mysql55-server                         x86_64
   5.5.9-1.ius.el5                          ius
     12 M
Installing for dependencies:
 mysqlclient15                          x86_64
   5.0.91-1.ius.el5                         ius
    1.7 M

Transaction Summary
==================================================================================================================================================
Install       4 Package(s)
Upgrade       0 Package(s)

Total download size: 22 M
Is this ok [y/N]: y
Downloading Packages:
(1/4): mysql55-libs-5.5.9-1.ius.el5.x86_64.rpm
                                                       | 1.2 MB
00:00
(2/4): mysqlclient15-5.0.91-1.ius.el5.x86_64.rpm
                                                       | 1.7 MB
00:00
(3/4): mysql55-5.5.9-1.ius.el5.x86_64.rpm
                                                       | 7.4 MB
00:02
(4/4): mysql55-server-5.5.9-1.ius.el5.x86_64.rpm
                                                       |  12 MB
00:04
--------------------------------------------------------------------------------------------------------------------------------------------------
Total
                                              2.9 MB/s |  22 MB
00:07
Running rpm_check_debug
Running Transaction Test
Finished Transaction Test
Transaction Test Succeeded
Running Transaction
  Installing     : mysql55-libs

      1/4
  Installing     : mysqlclient15

      2/4
  Installing     : mysql55

      3/4
  Installing     : mysql55-server

      4/4

Installed:
  mysql55.x86_64 0:5.5.9-1.ius.el5            mysql55-libs.x86_64
0:5.5.9-1.ius.el5            mysql55-server.x86_64 0:5.5.9-1.ius.el5


Dependency Installed:
  mysqlclient15.x86_64 0:5.0.91-1.ius.el5



Complete!
[root@mysql55 ~]# mysql
Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 2
Server version: 5.0.77 Source distribution

Copyright (c) 2000, 2010, Oracle and/or its affiliates. All rights
reserved.

Oracle is a registered trademark of Oracle Corporation and/or its
affiliates. Other names may be trademarks of their respective
owners.

Type 'help;' or '\h' for help. Type '\c' to clear the current input
statement.

mysql> Bye
[root@mysql55 ~]# chkconfig --list mysqld
mysqld          0:off   1:off   2:off   3:off   4:off   5:off   6:off



The fact that the service was not originally stopped by rpm -e mysql is not really a bug with this package set but I would still expect a conditional restart to dodge that bug.