Are there any tools out there that parse smali code directly to construct CFG? I know that Androguard does something similar but it seems to use decompilation on the apk file which can become unreliable in situations if the apk uses obfuscation techniques.
Building a Control Flow Graph for Android APK from smali code
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Have a look at https://androguard.blogspot.co.il/2011/02/android-apps-visualization.html.
In regards to your concerns about Androguard.
Do you mean "disassembling"? Well, a tool needs to understand the bytecode in order to build a call graph. If you mean "decompiling to Java", I'm pretty sure this doesn't happen.
There are various obfuscation techniques. And most has nothing to do with the call graph. E.g. name mangling replaces class name like
org.apache.http.client.HttpClientto something meaningless likea.b.c. You will still see this class and its functions in CFG.