Одна опция состояла бы в том, чтобы поместить переписать правила в различные блоки <VirtualHost>. например:
<VirtualHost *:80>
ServerName www.redirectsite1.com
RewriteEngine On
RewriteRule ^$ http://targetsite.com/search.html?state=PA&id=75 [QSA,R,L]
RewriteRule ^PGN$ http://targetsite.com/search.html?state=PA&id=26 [QSA,R,NC,L]
RewriteRule ^NS$ http://targetsite.com/search.html?state=PA&id=27 [QSA,R,NC,L]
RewriteRule ^INQ$ http://targetsite.com/search.html?state=PA&id=28 [QSA,R,NC,L]
RewriteRule ^AA$ http://targetsite.com/search.html?state=PA&id=29 [QSA,R,NC,L]
RewriteRule ^PI$ http://targetsite.com/search.html?state=PA&id=30 [QSA,R,NC,L]
RewriteRule ^GV$ http://targetsite.com/search.html?state=PA&id=31 [QSA,R,NC,L]
# catch-all rule, using the same id as the organic visit
RewriteRule ^([a-z]+)?$ http://targetsite.com/search.html?state=PA&id=75 [QSA,R,NC,L]
</VirtualHost>
<VirtualHost *:80>
ServerName www.redirectsite2.com
RewriteEngine On
# rule for organic visit first
RewriteRule ^$ http://targetsite.com/search.html?state=NJ&id=68 [QSA,R,L]
RewriteRule ^SL$ http://targetsite.com/search.html?state=NJ&id=6 [QSA,R,NC,L]
RewriteRule ^APP$ http://targetsite.com/search.html?state=NJ&id=8 [QSA,R,NC,L]
# catch-all rule, using the same id as the organic visit
RewriteRule ^([a-z]+)?$ http://targetsite.com/search.html?state=NJ&id=68 [QSA,R,NC,L]
</VirtualHost>
Другая опция состояла бы в том, чтобы поместить RewriteCond %{HTTP_HOST} ^www\.redirectsite1\.com$
перед каждым RewriteRule для сайта 1 и RewriteCond %{HTTP_HOST} ^www\.redirectsite2\.com$
перед каждым RewriteRule для сайта 2.