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From
http://dev.eclipse.org/viewcvs/index.cgi/platform-vcm-home/docs/online/html-cvs/cvs-compatibility.html?rev=1.5:

* Eclipse has an extssh connection method which uses an

internal SSH client. This method is incompatible with other
CVS clients. To avoid this, users can configure the ext
connection method in Eclipse to use the extssh connection
method by choosing this option on the Team>CVS>EXT
Connection Method preference page. Once set, the user can
create repository locations using the ext connection method.
These repositories will use extssh inside Eclipse and
whatever SSH tool is configured for the command line client.

FYI, since TortoiseCVS is a frontend to the standard CVSNT
client, it is not technically possible to implement your
suggestion.