Hi,
if you can set that meta tag in sharepoint that is fine, but you might end up breaking sharepoint functionality by doing that. One workaround is to open the webdynpro apps in new windows, I assume that you are embedding them in sharepoint e.g. In an iframe. The other thing I would look into is the webdynpro version you are on, a recent patch my include better support for standards mode.
hth,
simon