If you want the page numbers to be formatted differently to the text then manual formatting is the only way to go at the moment. You can set a style to be used when generating the TOC but it applies to the whole entry including both text and number.
My usual recommendation is to wait until the document is finished - or up to the point that the TOC won't change - and then re-format as necessary. Regenerating the TOC will overwrite any formatting changes in the text frame that you told Scribus to generate the TOC in so copying the generated text to a different frame would stop it from being overwritten (possibly accidentally).
One procedure you could follow would be to:
* Find the space you want to put the TOC frame in.
* Create a new layer - e.g. "GeneratedTOC".
* Create the text frame to generate the TOC in on this new layer.
* Set the TOC to generate in this frame.
* Edit your document in your "normal" layers as necessary, generating the TOC as needed.
* When you're finished editing, go back to the "GeneratedTOC" layer.
* Copy the TOC frame - Edit -> Copy.
* Go beck to your "normal" text layer.
* Paste the frame over the area where the generated TOC is.
* Set the "GeneratedTOC" layer to be not visible and not exportable.
* Edit the pasted frame - in the "normal" text layer - as necessary.
This way, you still have a way of re-generating the TOC if absolutely necessary and temporarily setting the "GeneratedTOC" layer back to visible will quickly show you what changes you need to make to the copied version.
It's a bit long-winded but it might come in useful.