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Of course their employees will not directly attack US legislators. But YES, it sounds very much like a threat; a call to action for others to attack US senators who vote for future Justice Kavanaugh.

Like many other organizations: ACLU and the NRA for instance, the political action arm is separately organized.

".....Planned Parenthood's advocacy activities are executed by the Planned Parenthood Action Fund, which is registered as a 501(c)(4) charity, and files financial information jointly with PPFA. The committee was founded in 1996, by then-president Gloria Feldt, for the purpose of maintaining reproductive health rights and supporting political candidates of the same mindset. In the 2012 election cycle, the committee gained prominence based on its effectiveness of spending on candidates. Although the Planned Parenthood Action Fund (PPAF) shares some leadership with the Planned Parenthood Federation of America, the president of PPAF, Cecile Richards, testified before Congress in September 2015 that she did not manage the organization."

The 501(c)(4) is not a deductible charity and likely receives no Federal funds. Hence, they maintain that thin line separating the baby killers (reproductive health care providers as they call themselves with a smile) and the Action Fund which issued this veiled threat.