Nice questions! The answers are no in both cases, although the examples are more interesting than one would expect.
1) Even when $A$ is regular, one can always find an ideal $I$ with $3$ generators such that $A/I$ has depth $0$. This is due to a very nice result by Bruns, which says you can construct $3$-generated ideal with all kinds of homological patern. The details are explained in this answer.
2) Let $R=k[X^4,X^3Y,XY^3,Y^4]$. Then $R$ is a domain of dimension $2$ which is not Cohen-Macaulay. So one can write $R=S/Q$, where $R=k[a,b,c,d]$ and $Q$ is a prime ideal of height 2. Take $(f,g)$ to be a regular sequence in $Q$ and let $I=(f,g)$. Then $A=S/I$ is Cohen-Macaulay (being a complete intersection), but $Q$ is a minimal prime of $A$ and $R=S/Q$ is not CM.