You're leaping too quickly to the attempted formalization; the informal passage in question needs further analysis.
Basically, a passage like
"We claim that $X$. To obtain a contradiction, assume $Y$"
is shorthand for
"We claim that $X$. To prove this, suppose $\neg X$. Then because [reasons], we have $Y$."
The original passage has two implicit claims:
The first point is simple enough, but the latter can be problematic: it's only really appropriate if we can "easily" prove $\neg X\rightarrow Y$ to the point that it's not worth mentioning. Whether or not a given usage is appropriate is of course subjective.
So, for example, the first argument in the linked text "unfolds" to the following:
Claim: If $X$ is a poset in which every chain has an upper bound, then $X$ has a maximal element.
Proof: Suppose not. Let $X$ be a counterexample. Then $X$ has no maximal element, so $[\mathit{stuff}]$. But that gives us a chain in $X$ with no upper bound, which can't happen because $X$ - being a counterexample to the claim - must have the property that every chain has an upper bound.
Somewhat more formally, this amounts to something like the following:
Begin subproof:
Assume $\neg(\forall X[\mathit{chainbound(X)}\rightarrow\mathit{maxelt(X)}])$.
Then $\exists X[\mathit{chainbound(X)\wedge\neg maxelt(X)}]$.
Do existential instantiation - introducing a specific counterexample $C$.
In particular, $C$ has no maximal element.
Deduce $\perp$.
Discharge the assumption so that we get $\neg(\forall X[\mathit{chainbound(X)}\rightarrow\mathit{maxelt(X)}])\rightarrow\perp$.
From that, conclude $\forall X[\mathit{chainbound(X)}\rightarrow\mathit{maxelt(X)}]$.
Of course that's neither complete ("Deduce $\perp$" :P) nor correctly formed (exactly how subproofs/discharging assumptions are presented will be determined by the system you're using), but it should suggest how to proceed.