Setting the scene
Your central point is, given Bentham's account of psychology, 'considering guilt as pain then wouldn't we naturally behave in a morally permissible way'? But on this scenario it doesn't follow that guilt causes enough pain in the scheme of pleasures and pains to stop me from continuing whatever it is that is causing the pain or from doing it again.
Bentham offers a longer route to ensuring or encouraging morally permissible (or mandatory) behaviour. It involves sanctions.
To begin, guilt can play a role only as an episode or state of pain or pleasure. I feel guilty, and it 'hurts'. Accept that, for now.
In the passage you quote, Bentham refers to pain and pleasure. Specifically, he means the pain and pleasure of the agent. This self-interested focus is particularly clear in Bentham's Deontology :
When the happiness of others as well as his own is at stake upon the conduct
he is about to pursue, a man's own happiness it has already been observed will
be the sole ultimate as well as immediate object of his solicitude; that of others, no further than insofar as his own happiness is affected in virtue of the
way in which the happiness of others is affected by his conduct. (D, 123)
I can be affected by and respond to your pains and pleasures but only because their occurrence causes me pain or pleasure.
Then, for Bentham the individual person will, and is pre-determined to, pursue her or his personal utilities. Bentham does not appeal to conscience or a sense of duty as a source of pleasure and pain. Specifically, he does not posit a sense of guilt as causing pain.
Even if he had or did, it would not follow (to reword from above) that the intensity of the pain of guilt would outweigh the pleasure of guiltily doing what one wants to. The pain of guilt would be only one variable in deciding what to do or in judging what one has done.
We can agree that 'Act for yourself' summarises Bentham's ethics of personal life. But we live with others, and there is a public or community good from which we can and do benefit but which can't be secured if 'Act for yourself' - look out for your own pleasures and pains - is unchecked. Bentham is keenly aware of public or community good.
The legislator, the government or public power, charged with promoting the public or community good, has to check personal egoism so as to secure those interests of mutual benefit which will be lost - forgone - unless individuals are induced to practise a degree of altruism. Hence Bentham's comment: 'The business of government is to promote the happiness of the society, by punishing and rewarding' (The Principles of Morals and Legislation, ch. VII.)
At this point sanctions come into play. The pursuit of private good is deflected towards altruism by making altruism - not total altruism but enough to secure the public good - pay. It pays because of the sanctions or penalties that are imposed on diverse, self-interested and antagonistic personal utilities; there is more painful consequence to the individual in pursuing personal utility and private good over a range of actions than in complying with the requirements of the public or community good.
Sanctions reconcile personal and public good by so contriving matters that personal utility can be maximised only if individual conduct is self-constrained to avoid the sanctions or penalties incurred by not heeding the public or community good.
Bentham, Jeremy. 1983/ posth. 1834. Deontology together with A Table of the Springs of Action and The Article on Utilitarianism, ed. Amnon Goldworth. New York: Oxford University
Press. ISBN 10: 0198226098 ISBN 13: 9780198226093.
Bentham, Jeremy, An Introduction to the Principles of Morals and Legislation (printed 1780, published 1789): https://socialsciences.mcmaster.ca/econ/ugcm/3ll3/bentham/morals.pdf.
Hocutt, Max, 'Was Bentham a Utilitarian?', Canadian Journal of Political Science / Revue canadienne de science politique, Vol. 38, No. 3 (Sep., 2005), pp. 697-717.