Inside the FOP2 configuration file (/usr/local/fop2/fop2.cfg) you can pass different parameters to chan spy when the whisper action is launched, that is all you can change in FOP2 config but I do not think that any parameter in ChanSpy would modify or alter that noise you hear. The default setting is:

whisper_options="w"

You can modify it, for example to avoid playing a beep, add the option "q"

whisper_options="wq"

Here is the list of options available on Asterisk 13:

[Arguments]
options
    b: Only spy on channels involved in a bridged call.

    B: Instead of whispering on a single channel barge in on both channels
    involved in the call.

    c(digit): 
        digit - Specify a DTMF digit that can be used to spy on the next
        available channel.


    d: Override the typical numeric DTMF functionality and instead use DTMF to
    switch between spy modes.
        4 - spy mode
        5 - whisper mode
        6 - barge mode

    e(ext): Enable *enforced* mode, so the spying channel can only monitor
    extensions whose name is in the <ext> : delimited list.

    E: Exit when the spied-on channel hangs up.

    g(grp): 
        grp - Only spy on channels in which one or more of the groups listed in
        <grp> matches one or more groups from the ${SPYGROUP} variable set on
        the channel to be spied upon.
NOTE: both <grp> and ${SPYGROUP} can contain either a single group or a
colon-delimited list of groups, such as 'sales:support:accounting'.

    n([mailbox][@context]): Say the name of the person being spied on if that
    person has recorded his/her name. If a context is specified, then that
    voicemail context will be searched when retrieving the name, otherwise the
    'default' context be used when searching for the name (i.e. if SIP/1000 is
    the channel being spied on and no mailbox is specified, then '1000' will be
    used when searching for the name).

    o: Only listen to audio coming from this channel.

    q: Don't play a beep when beginning to spy on a channel, or speak the
    selected channel name.

    r([basename]): Record the session to the monitor spool directory. An
    optional base for the filename may be specified. The default is 'chanspy'.

    s: Skip the playback of the channel type (i.e. SIP, IAX, etc) when speaking
    the selected channel name.

    S: Stop when no more channels are left to spy on.

    u: The 'chanprefix' parameter is a channel uniqueid or fully specified
    channel name.

    v([value]): Adjust the initial volume in the range from '-4' to '4'. A
    negative value refers to a quieter setting.

    w: Enable 'whisper' mode, so the spying channel can talk to the spied-on
    channel.

    W: Enable 'private whisper' mode, so the spying channel can talk to the
    spied-on channel but cannot listen to that channel.

    x(digit): 
        digit - Specify a DTMF digit that can be used to exit the application
        while actively spying on a channel. If there is no channel being spied
        on, the DTMF digit will be ignored.


    X: Allow the user to exit ChanSpy to a valid single digit numeric extension
    in the current context or the context specified by the ${SPY_EXIT_CONTEXT}
    channel variable. The name of the last channel that was spied on will be
    stored in the ${SPY_CHANNEL} variable.

Best regards,

FOP2 does not handle audio in any way, all audio processing is done by Asterisk. Noise is usually not a problem, unless you have some analog part in the middle, from your report I will suspect of analog noise introduced (loose cable somewhere), that will get through on whispering or any other conversation for that matter.

As FOP2 does not do audio processing, you will have to look into the Asterisk side of things for the problem.

Best regards,