The comma after obstacle does not stand for the word and. The phrase “when they meet with an obstacle” is parenthetical* and is marked front and back with commas.
The inverted word order used in many places in the poem creates some confusion. Also complicating the issue is that early versions of the poem contain a grammatical error. Where you have:
As dry leaves before the wild hurricane fly,
When they meet with an obstacle, mount to the sky;
So up to the house-top the coursers they flew,
Later versions read:
As dry leaves that before the wild hurricane fly,
When they meet with an obstacle, mount to the sky;
So up to the house-top the coursers they flew,
It may help to see the text prosaically reordered and the parenthetical phrase marked with parentheses:
As dry leaves that … fly before the wild hurricane
… Mount to the sky (when they meet with an obstacle);
So … the coursers they flew up to the house-top,
Wikisource describes the poem’s history and reproduces the published variants of the text.¹
Footnotes
* This statement has been challenged, so here I explain why – though its absence would be detrimental to the meaning of the verse – the phrase “when they meet with an obstacle” is quite properly described as parenthetical: it interrupts the grammar of the sentence, and is set apart in print with commas as befits its importance.
The dictionary describes a parenthesis as “[a] word, phrase, or sentence, by way of comment or explanation, inserted in, or attached to, a sentence which would be grammatically complete without it [emphasis added]”.² That is, a parenthesis contributes to the semantics (meaning) of the sentence but interrupts and stands beside (independent of) the syntax (grammar, structure) of the sentence. Wikipedia derives the word from the Greek παρένθεσις, meaning “to place alongside of”.³
In print, a parenthesis is set apart from the enclosing sentence using punctuation. When it is not an important insertion, square brackets or curved lines called parentheses are commonly used; for greater importance or emphasis, commas or even dashes are used.⁴
(Bold face is used in this note to mark parenthetical text.)