You can do this without disabling SIP by creating a copy of the system RichText.mdimporter, modifying its Info.plist and saving it in /Library/Spotlight.
cp -r /System/Library/Spotlight/RichText.mdimporter .
patch -p2 RichText.mdimporter/Contents/Info.plist < Markdown.patch
mv RichText.mdimporter Markdown.mdimporter
sudo cp -R Markdown.mdimporter /Library/Spotlight
mdimport -r /Library/Spotlight/Markdown.mdimporter
Markdown.patch
diff -ru RichText.mdimporter/Contents/Info.plist Markdown.mdimporter/Contents/Info.plist
--- RichText.mdimporter/Contents/Info.plist 2015-11-23 16:14:12.000000000 +0200
+++ Markdown.mdimporter/Contents/Info.plist 2015-11-23 16:10:03.000000000 +0200
@@ -13,15 +13,7 @@
<string>MDImporter</string>
<key>LSItemContentTypes</key>
<array>
- <string>public.rtf</string>
- <string>public.html</string>
- <string>public.xml</string>
- <string>public.plain-text</string>
- <string>com.apple.traditional-mac-plain-text</string>
- <string>com.apple.rtfd</string>
- <string>com.apple.webarchive</string>
- <string>org.oasis-open.opendocument.text</string>
- <string>org.openxmlformats.wordprocessingml.document</string>
+ <string>net.daringfireball.markdown</string>
</array>
</dict>
</array>
@@ -30,11 +22,11 @@
<key>CFBundleGetInfoString</key>
<string>1.0, Copyright (c) 2004-2010 Apple Inc.</string>
<key>CFBundleIdentifier</key>
- <string>com.apple.MDImporter.RichText</string>
+ <string>com.apple.MDImporter.Markdown</string>
<key>CFBundleInfoDictionaryVersion</key>
<string>6.0</string>
<key>CFBundleName</key>
- <string>Rich Text Sniffer</string>
+ <string>Markdown Sniffer</string>
<key>CFBundleShortVersionString</key>
<string>6.9</string>
<key>CFBundleSupportedPlatforms</key>