Consider a partially ordered set $(X,\leq)$. For finite subsets $A,B\subseteq X$, write $A\preceq B$ whenever there is an injection $f:A\to B$ such that $a\leq f(a)$ for every $a\in A$.
It is easily seen that the finite subsets of $X$ are now quasi-ordered by $\preceq$, that is, $\preceq$ is a reflexive and transitive relation.
I am wondering if the antisymmetry of $\leq$ now also extends to $\preceq$?
Yes, it does. It may be easiest to reason by induction. Note that if $A \leq B$ and $B \leq A$ then $|A| = |B|$. Trivially it is true for $A, B$ empty. Now suppose that our statement is true for all subsets smaller than $A, B$.
Suppose that $A, B$ are such that $A \leq B$ and $B \leq A$ by your definition, witnessed by $f: A \to B$ and $g: B \to A$. Now take $a \in A$ and consider $a \leq f(a) \leq g(f(a)) \leq f(g(f(a))) \leq \cdots$. This is an infinite increasing sequence in the set $A \cup B$, and thus must eventually repeat, let's say starting at element $b$. Because $\leq$ is anti-symmetric, it follows that we find $b = f(b) = g(f(b))$. Then we can consider $A \setminus \{b\}$ and $B \setminus \{b\}$, and restricting $f, g$ to those sets still gives us that $A \setminus \{b\} \leq B \setminus \{b\}$ and vice versa. But by the induction hypothesis, it follows that these sets are equal. Thus they are also equal when $b$ is added back in, completing the proof by induction.