In short, you tried to nest string quoted with single-quotes. That doesn't work. What follows is what bash see and how to fix the problem without changing what Perl sees.

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To form the string from the literal

'if (-d "/usr") { print 'yes';}'
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bash extracts what's in single quotes and concatenates it with what's not in quotes. That means the following are concatenated together:

1. if (-d "/usr") { print (not subject to interpolation and unescaping)
2. yes (subject to interpolation and unescaping)
3. ;} (not subject to interpolation and unescaping)

Let's use Perl to see how bash sees the command:

$ perl -le'print "[$_]" for @ARGV' -- \
    perl -le 'if (-d "/usr") { print 'yes';}'
[perl]
[-le]
[if (-d "/usr") { print yes;}]
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Compare with:

'if (-d "/usr") { print '\''yes\''';}'
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1. if (-d "/usr") { print (not subject to interpolation and unescaping)
2. \' (subject to interpolation and unescaping)
3. yes (not subject to interpolation and unescaping)
4. \' (subject to interpolation and unescaping)
5. ;} (not subject to interpolation and unescaping)

$ perl -le'print "[$_]" for @ARGV' -- \
    perl -le 'if (-d "/usr") { print '\''yes'\'';}'
[perl]
[-le]
[if (-d "/usr") { print 'yes';}]
[download]