Because they're also lobbying for other things you care about. And those things are more likely to be passed into law than the E2E encryption pieces.
Taking a puritanical view on an issue is a high-risk high-reward gambit. Nine out of ten times, it ejects you from the room. One out of ten times, you will organize sufficiently to make it a wedge issue (e.g. the NRA on guns, NIMBYs, et cetera).
To the extent Haugen disagrees, she's not on "our side."
It's not reasonable to outlaw the tools needed to exercise a fundamental right. Not OK for the 1st, not OK for the 2nd, and not OK for the 4th. Encryption was already an old technology at the time of the Constitution's authorship. If they had wanted to regulate or outlaw it, they were free to say so. They didn't.
...so if they had wanted to guarantee a right to it, they were free to say so.
But they didn't.
Despite clearly contemplating privacy.
Depending on how terrible the bad ideas are that they're pushing, they may not be an ally at all in fact. A multi-purpose trojan horse may be more accurate.
In this case, promoting the abolition of end to end encryption is quite heinous. She's providing the authoritarians a potent argument that isn't yet well established in the public mind (we have to be able to see all of your data so we can keep you safe from the Chinese trying to see all of your data).
One doesn’t have to agree 100% with an ally.