There are two forms of the tomee webapp to consider:

The only real difference between a "Tomcat with drop-in tomee.war" and a "TomEE" install is where the additional libraries live.

Deleting from plain Tomcat

Deleting the tomee webapp from a plain Tomcat install will effectively uninstall TomEE from Tomcat.

Deleting from TomEE

Deleting the tomee webapp from a TomEE install is safe as the needed libraries have been moved into <tomcat-home>/lib/

The only loss of functionality would be the ability to remotely execute EJBs over HTTP. However this can easily be added to a different webapp like so:

<servlet>
  <servlet-name>ServerServlet</servlet-name>
  <servlet-class>org.apache.openejb.server.httpd.ServerServlet</servlet-class>
</servlet>

<servlet-mapping>
  <servlet-name>ServerServlet</servlet-name>
  <url-pattern>/myejbs/*</url-pattern>
</servlet-mapping>

Then you can create an InitialContext that points to that webapp like so:

Properties p = new Properties();
p.put("java.naming.factory.initial", "org.apache.openejb.client.RemoteInitialContextFactory");
p.put("java.naming.provider.url", "http://127.0.0.1:8080/mywebapp/myejbs");
// user and pass optional
p.put("java.naming.security.principal", "myuser");
p.put("java.naming.security.credentials", "mypass");

InitialContext ctx = new InitialContext(p);

MyBean myBean = (MyBean) ctx.lookup("MyBeanRemote");