A moratorium, forbearance or deferment -- these terms all mean the same thing -- means that your lender allows you to suspend making payments for a limited period of time. Lenders might do that if you experience a temporary setback, knowing that soon enough, you'll be able to resume repayment.
You are penalized because mortgage payments have a big effect on your FICO credit score and credit history. Missing mortgage payments does serious damage to your credit. Even if the lender approves this, your payments are likely to be reported as late, or your loan may be tagged with the code meaning that you have not repaid it as agreed.
Other things that might be considered penalties by some is the fact that the lender does require repayment -- you'll either have to "catch up" the past-due balances over time with a higher mortgage payment, or the lender adds the unpaid amounts to your loan balance. That results in a higher loan amount, higher payment and additional interest.
But if a moratorium, forbearance or deferment gets you out of a jam, be grateful. The lender COULD have initiated foreclosure proceedings instead. Fortunately, they hate foreclosures almost as much as borrowers do.