Sure, you can. Actually, the conflicts are possible as soon as browser do not know those are the same.
We try to keep the version of Prototype and Scriptaculous always up to date.
If you do not have any components that use them, you can include such library explicitly.

Prototype:

<a4j:loadScript src="resource://prototype.js" />

Scriptaculous:

<a4j:loadScript src="resource://scriptaculous.js" />

If you do not want to load the whole Scriptaculous, you can refer to the particular file, like:

<a4j:loadScript src="resource://scriptaculous/effects.js" />

Additional Info:

The above strings are aliases (shortcuts).

You can use the full name like:

<a4j:loadScript src="resource:///org/richfaces/renderkit/html/scripts/scriptaculous/effects.js" />

The list of aliases you can look at the /META-INF/resources-config.xml files located in richfaces-impl.xxxxx.jar

When it might be important:
javascript libraries extensions each other very often. The order of the libraries is important. I guess, you know it, as soon as already use them. So, if you load first library, extend it with the second one and them load the first library, but using different name - the browser load it and overwrite the extensions.

If you use the richfaces components, some of them load the libraries omplicitly. If you load the same library explicitly after that, the problem above might be possible.

So, if you suddenly get something like "variable is not defined", look at the page header and see for double loading. Removing the same lib (with diff path) or using the same path should help.