Yes, google's John Mueller has said that pages that return a 404 or a 410 would be treated similarly to a page where the links have been disavowed.
"However what would I do about the many links that are pointing to the homepage? That's the stumbling block"
Ideally, disavow them and have them removed. This is what you should be doing for ALL the bad links that point to your site's pages, EVEN IF YOU REMOVED THE PAGE.
Here is what I did / would do:
1) Disavow any questionable link.
2) Remove pages that had only bad links and put the content onto a new page.
3) Contact webmasters and ask them to remove those bad links to my site (keep accurate notes and copies of your emails to - and responses from - those webmasters.
4) You may have to wait until those pages that you removed are no longer showing in google's SERPs. That might be overkill, but if you have been submitting reconsideration requests too frequently, then maybe a little patience would be appreciated by the reconsideration team.
I don't have any proof, but judging by what the people who HAVE recovered from manual penalties or penguin have experienced:
1) New links will not be as effective at flowing page rank to your site as they would have been had you not had a previous penalty / been penguinized
2) Your site MIGHT be watched more frequently by the good people at google.